


Making You Better

by ChibiAyane



Series: My John Sheppard Challenge [4]
Category: Stargate Atlantis
Genre: Alien Sex, Explicit Sexual Content, F/M, Genderbending, Hermaphrodites, Human Experimentation, Hybrid John Sheppard, John Sheppard Whump, Kidnapping, Lust, M/M, Mpreg, Non-Consensual Kissing, Obsessive Behavior, Poor John, Possessive Behavior, Rape Aftermath, Rating is for later chapters, Sexual Harassment, Tags May Change, Tentacles, Wraith Hybrids, Xenobiology, gene manipulation
Language: English
Status: In-Progress
Published: 2020-01-24
Updated: 2020-02-25
Packaged: 2021-02-27 10:47:49
Rating: Explicit
Warnings: Graphic Depictions Of Violence, Rape/Non-Con
Chapters: 14
Words: 21,642
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/22385908
Author URL: https://archiveofourown.org/users/ChibiAyane/pseuds/ChibiAyane
Summary: Michael kidnaps John for nefarious reasons. What could he possibly want with him? Nothing John wants anything to do with. Too bad he doesn't get a choice.Please read tags. Will add more tags later.
Relationships: John Sheppard/Todd the Wraith, Michael Kenmore/John Sheppard
Series: My John Sheppard Challenge [4]
Series URL: https://archiveofourown.org/series/1415662
Comments: 50
Kudos: 144





	1. Taken

**Author's Note:**

> Special thanks to Eos1969 for being my beta.

Making You Better

They were running again. They couldn't even see who was shooting at them. Although, the blasts from wraith stunners should have been a clue. However, John Sheppard and his team have long since learned that wraith stunners didn't necessarily mean wraith. Even Atlantis used wraith stunners.

John turned and fired blindly into the dark woods. His team was ahead of him, as he brought up the rear, so there was no fear of hurting his friends.

He turned to continue his mad dash for the 'Gate. He was close enough to hear the whoosh of the wormhole forming, glad that McKay had gotten to it safely since he was at the head of the group. 

John looked over his shoulder one more time, but it was a mistake. He ran headlong into someone, knocking himself back onto his ass.

“What the...?” John started to ask but was stopped when there was a sharp pain in his neck. He still couldn't see who it was, it was so dark. He'd never gotten the chance to turn his flashlight on or dig out his night vision goggles as he was running.

It didn't matter though, because soon he was engulfed by a darkness no one could see through.

John woke up slowly. He had no idea how much time had passed. As he opened his eyes, he realized he had no idea where he was either.

He had a massive headache and when he tried to raise his hands to rub his temples, he found that he couldn't. Testing it out, he realized he was chained to a table. It felt like an operating table, having been on enough of those to know what they felt like.

It was dark in the room.

“Hello?” John called, his voice cracking from disuse. It was a relatively small room based on the echo. 

There was a small window in what he assumed was the only door. A very minimal amount of light shown through that small window.

“Hello!?” John called louder, rattling the chains on his wrists and the ones he realized were around his ankles.

“Hush now, John,” a voice said from only a few feet away. “You'll wake the children.”

“Jesus fucking Christ!” John gasped, jerking in surprise. “Don't do that!”

The voice laughed and moved closer. John tried to see who it was but it was too dark. The voice sounded familiar and strange. Almost wraith-like but not quite. 

John's stomach dropped when he figured it out. The dread built up in his belly, tensing his shoulders and causing him to struggle against the chains. 

“Michael?” John asked in a whisper.

“It's good to see you again, John,” Michael said, stepping up beside John.

John could just see his outline in the limited light. “Wish I could say the same, but I can't see a damn thing,” he drawled.

“It'll get better,” Michael said dismissively.

There was a poke in John's arm and he felt the burn of something being injected.

“What the hell was that?” the Colonel asked trepidatiously. 

“Gene therapy,” Michael answered simply.

“What?” John asked, freezing his attempts to get free. “Gene therapy for what?”

A hand brushed the hair back from John's forehead, and a soft chuckle filled John's ear. Michael's face was right beside John's.

“I'm going to make you into a very special kind of hybrid,” Michael spoke gently into John's ear, his hand petting the Colonel's hair.

“No,” John said softly, almost begging. “You can't do that!”

“It's already started,” Michael said.

“Why me?” John growled.

“Many reasons,” Michael answered.

“What are you turning me into?” John whispered.

“Did you know that most wraith queens are hermaphrodites?” the hybrid asked.

John frowned. “No, I did not know that. What does that have to do with me?”

“And did you know that the Iratus bug that bit you was a female?” Michael continued. “It's all there in your blood. Dr. Beckett made note of it.”

“Why does that matter?” John asked, getting very confused and frustrated by the direction this conversation was taking.

"You were stung by a female wraith that had been exposed to Iratus RNA," Michael kept talking, ignoring John's queries. "You nearly turned into a human-Iratus hybrid." 

Michael's hand moved down and caressed John's face. John jerked his face away from the offending hand.

“You're not answering me!” John spat, a little disturbed that Michael knew so much.

“Actually, I am,” Michael said with a condescending smile in his voice. “Put the pieces together, John. You're smart enough. Stop playing dumb. I read your files when you had me locked up in that made up life on Atlantis.”

John gulped, a slow panic building up in his shoulders. “Why did you read my files?” he asked lowly, deflecting for now. 

Michael chuckled, knowing exactly what he was doing. The hybrid brought his hands to either side of John's face and rubbed his thumbs over John's cheekbones. The darkness of the room didn't seem to bother or deter Michael from studying his captive. 

“I had no memory of anything, no family, no friends, no lovers. But I still understood desire and lust,” Michael said, scaring the crap out of John. “I desired you from the moment I first saw you. Naturally, I would want to learn everything I could about you.”

“The creepy way,” John drawled, trying to sound less terrified. He knew he was failing horribly.

Michael made a sound like he was amused, his thumbs stroking John's cheeks again. With no warning whatsoever, Michael's lips claimed John's. John gasped and Michael used the chance to push his tongue into the Colonel's mouth. For several moments, John was too stunned to do anything. When he got it in his head to bite, Michael pulled back. With one more flick of his wet tongue over John's pouty bottom lip, Michael pulled away completely.

“You taste better than I thought you would,” Michael commented, panting and out of breath.

John growled, trying to keep his mouth in check. 

“You've figured it out, John. I know you have,” Michael continued. “So what do I plan on doing to you?”

John glared at what he could see of Michael's form. “Turn me into a weird human-wraith-Iratus bug hybrid hermaphrodite freak,” he growled through clenched teeth. “I'm guessing.”

"You guess correctly," the hybrid said. "I'm going to turn you into the perfect mate for me. It would please me and make my work much simpler. So I see no reason to refrain from taking something I've wanted for a long time." 

"Wait," John gasped, disgust settling in the pit of his stomach. "You're not going to make me lay eggs or something, are you?" 

“I don't know for sure,” Michael said with a tilt of his head. “There's a fifty-fifty chance of you gestating like a wraith or like a human.”

“Get the fuck away from me!” John yelled, renewing his struggles against his restraints.

Michael laughed again, then crushed his lips to John's one more time. He licked and explored John's lips with his tongue, even though John kept trying to turn his face away or bite him. But Michael simply held John's face in his hands, pulling back and smirking each time John's teeth came at him. The hybrid finally pulled back, sighing softly.

“Soon enough, we'll be able to enjoy each other's bodies,” Michael lamented. “But not yet.”

“No chance!” John hissed.

“You'll change your mind,” Michael said confidently. He stood from his lean over John. “Let me know when it gets easier to see,” he instructed. “Just scream. One of the children will hear you.”

“Children?” John asked.

“My hybrids,” Michael informed, then left the room through the door with the dusty window.

To be continued.  
I mean it this time, I swear!


	2. Changed

**Summary for the Chapter:**

> John's hell continues.

Chapter 2

After at least an hour of pulling at the chains fruitlessly, John passed out from exhaustion. When he woke, he found it wasn't so dim in the small room. John looked around for the new source of light, but when he realized there wasn't one, his blood froze. He suddenly felt like he was going to puke.

He was being turned into that thing again. Or something like it.

John just managed to turn his head toward the edge of the table before he coughed up nothing but bile. He didn't know how long ago it was that he'd shared that MRE with Teyla, so he wasn't surprised when he didn't bring up any undigested food.

It was only moments later that the door opened and Michael walked in with another hybrid. The unnamed hybrid had a towel and quickly cleaned up John's mess, then left again. 

Michael stood watching John carefully. “You can see me,” he stated. “You're following me with your eyes. So the therapy is working.” He sounded so hopeful, John almost wanted to puke again.

“Go to hell,” John spat.

Michael only laughed, then walked over and turned the overhead light on. John blinked at the sudden brightness, Once his eyes adjusted, he looked around to find he was in a small laboratory. 

Dread swelled deep in John's chest like an immovable lump of stone.

“Please don't do this to me,” John practically begged.

“It's too late for that,” Michael said, going to a piece of machinery that looked like a cross between wraith tech and Earth tech. Even his lab tools and computers were hybrids.

John mentally sighed, not sure he wanted to know how he'd gotten his hands on Earth tech.

“Just let me go!” John growled

“Not going to happen,” Michael said, turning to John with a smile. “I've been preparing for your arrival for a long while. I won't let you go now that I have you.”

“You're insane,” John sighed. “You know that?”

“Perhaps,” Michael allowed. “But you'll be like-minded soon enough.”

Michael went over to John with a needle in hand. John tried to jerk away.

“Be still,” Michael said, grasping John's arm and injecting him with something that burned like before. “You're dehydrated, I may need to put in one of the Earth I.V.s to give you fluids. Perhaps that would be best. I can more easily inoculate you if I do,” Michael continued, despite John's silent seething. “It might even speed up the process.” He turned and silently walked out, not waiting for a response.

John went back to pulling at the chains holding him, ignoring the pinch of the metal against his skin.

Michael returned a few minutes later with an I.V. pole and other medical instruments, wraith and Earth tools alike.

“Enough of that now,” Michael said, reaching to still John with a hand on his chest. “Injuries may have an adverse effect on the changing process.”

“Oh no! I wouldn't want to make it harder for you to turn me into an insect!” John yelled.

“Not an insect, John,” Michael said, smirking. “A queen.”

“I'm not supposed to be a queen of any kind!” John spat. “Cross-dressed, slimy green or otherwise!”

Michael ignored John, he simply turned, grabbed a tourniquet and tied it around John's bicep. He found a vein easily and pushed a needle into it. The tubing was a weird wraith kind of thing. Like the tubes, you found in a wraith computer terminal. It wasn't completely opaque, so, John could still see a milky looking liquid racing through it and into his body. 

“No, no no no,” John chanted softly, trying to pull at the restraints again.

“Stop doing that or I will have to inject you with something to keep you from moving,” Michael threatened.

The hybrid brought over another wraith instrument and stuck a weird fleshy lead to John's temple. 

“To monitor your brain waves,” Michael supplied, even though John didn't ask.

In fact, John was still chanting his mantra of 'no no no' under his breath. Very suddenly, John yanked violently on the chains, managing to break one hand free. Michael was there instantly, wrestling John's arm back down. 

Once Michael hand John's wrist secured again, John growled in frustration. He still struggled to get free, even though he was damaging his wrists in the process.

“Please don't turn me into that thing again!” John begged. “I'll do anything!”

“Tempting, John,” Michael hummed, coming toward John with a needle full of a greenish liquid. He pushed the liquid into the I.V. tube, then set it aside. “But I'm already getting what I want.”

John's vision dimmed around the edges and his body seemed to slump out of its tension. “What?” he slurred.

“It's a mild paralytic designed for wraith,” Michael said. He leaned in to look at John's face closer, inspecting his stillness in satisfaction. 

Michael hummed in appreciation, then grinned mischievously.

The hybrid held John's face in both hands as he'd done before. The soldier's unresistant body only gave Michael more ideas. That was for later though. 

He looked into John's glazed but furious eyes for a moment, then leaned in to seal his lips over John's, pushing his tongue into the slackened mouth. His tongue explored, mapped and plundered his intended's mouth. 

Michael began purring at one point. The kiss was absolutely filthy, Michael's tongue laying claim to John's. Their saliva mixed and Michael couldn't taste anything but John Sheppard. 

The hybrid pulled back for a single breath, changing his angle and diving in for another taste of his future mate.

John groaned, wanting to turn away from the violation, but whatever Michael gave him was keeping him as weak as a baby. He couldn't move much more than his fingers and eyes. So, of course, he couldn't stop the wraith-human hybrid from practically fucking his mouth with his tongue, when finished counting his teeth with the slick appendage. 

Michael's hands suddenly started moving over John's body seemingly of their own accord. Michael moaned, his hands finding their way to John's hips.

Then it was all over faster than it started, Michael's lips were gone along with his hands. Michael slowly composed himself, licking his kiss swollen lips.

“Your body is giving off the hermaphroditic pheromones already,” Michael said. “I'll need to keep better watch over the children.”

John wanted to tense as he tried to catch his breath. He whimpered, unable to move or yell or scream and bitch at Michael for the fresh hell he'd tossed him into.

Michael turned away, moving to the wraith computer terminal. He turned back with yet another wraith implement. John had no idea what it was. Michael grabbed the hem of John's standard black t-shirt and ruched it up until John's chest was exposed. He pressed the weird-looking sort of organic electrode to John's chest, just over his heart. The things seemed to fuse with John's skin. 

“To monitor your progress,” Michael said, his voice still a little shaken. “Since your body seems to be responding to the therapy better than I'd hoped.”

John didn't want to know what else Michael was going to do, and couldn't ask him to shut up even though he really wanted to. He wanted nothing more than to shoot the bastard in the face and go home.

Michael went over to another corner of the lab and came back with another needle full of some unrecognizable substance. He injected it into the I.V. tube slowly. John felt a cold sensation race through his body.

“Female Iratus hormones,” the hybrid said, terrifying John with every word he spoke. “To help control your gender change.”

John felt tears pricking the corners of his eyes. He could do nothing to stop this mad man from changing his body irreparably. He could do nothing but lay there, listening to the mad scientist talk his way through what he was doing to John.

John closed his eyes, the only part of his body that could still move, and let his physical and mental exhaustion take him away from the insanity. Just for a little while.

To be continued.

**Notes for the Chapter:**

> None of this was betaed. Seriously, all I did was read through it once and run it through Grammarly. =) All mistakes are mine.


	3. Violated

**Summary for the Chapter:**

> Michael's instincts take him too far.

Making You Better Chapter 3

John was awoken by fire. The intense burning coursing through his body and wrapping around his mind until knew nothing but the flames that seemed to flare from his belly. He heard someone screaming, only to realize it was he who was screaming in agony. He writhed in his chains, only mildly aware of the hands trying to hold him down. The flames were never-ending and he couldn't get away from them.

He felt a poke in the side of his neck and was swallowed by darkness once more.

John awoke again, feeling like his head was stuffed with cotton. His belly burned still, but nowhere near like it had before.

He turned his head and looked around dazedly. He saw Michael hunched over a work station.

“What did you do to me?” John groaned, voice scratchy and sore from screaming.

Michael turned around so fast, John was amazed he didn't fall over. The hybrid came over and caressed John's cheeks with both hands.

“How do you feel?” Michael asked eagerly.

“Like I just got hit by a truck,” John answered, then frowned. “You don't even know what a truck is.”

Michael hummed, observing John's face for a few moments. One of his hands trailed down from John's face. “The most difficult and important part of your transformation is complete,” he said, the hand that was moving down came to a stop over John's abdomen, just above his groin where there was still a shadow of the same burning that had engulfed him earlier.

“No,” John said slowly. “No!”

“Yes,” Michael said with a broad smile. “Your change is coming along nicely.” Michael's hand rubbed John's belly gently. “You should see yourself. The visible changes are remarkable. You're beautiful, John.”

“Go jump through a space 'Gate!” John said softly, the fight taken out of him by his transformation. He would've spat it out with more venom, but he was too tired for that.

Michael snorted quietly, still studying John's rapt interest. “It won't be long now,” he said. “On the bright side, I can tell you for sure, now, that you won't be laying any eggs.”

John glared at Michael hard.

“You will bear children the way any human female would,” the hybrid continued with a sense of glee. “I can't wait to see you with a swollen belly.”

“Never gonna happen,” John growled.

“Oh, it will,” Michael countered before turning away. “You'll be interested to know that your friends are searching for you frantically. They've even enlisted the help of the Genii and they've contacted the wraith who cooperates with you. What do you call him? Todd?”

He turned back toward John. “They're not even close to finding you. You're not on any planet the Atlantians have ever ventured to. The Wraith avoid this planet because it is uninhabited. The Genii do not know of it for the same reason. There is but one Ancient outpost here that we are currently in, but I don't foresee any of them even giving a planet like this a second thought.”

John ground his teeth. “You son of a bitch,” he hissed, tears pricking his eyes again, even as he seethed with rage.

Michael moved to hold John's face in his hands again. “No need to fret. You're safe with me.”

“We have very different concepts of what 'safe' means,” John hissed.

“You will want for nothing, John,” Michael tried to reassure. “You will have hybrids begging to take orders from you and humans who will worship the ground you walk on. You will have a devoted mate, with whom you will have many children.”

“I don't want any of that!” John spat.

“You will,” the hybrid countered.

“God, why are you doing this to me?” John groaned.

“Isn't it obvious?” Michael asked with a frown.

“No,” John said. “You never quite answered that question!”

Michael simply sighed, though he looked uncomfortable with the subject. “You'll figure it out.”

He leaned in and stole a kiss from John. It was a quick one, as John almost bit him.

"I can't wait for when you'll want to kiss me back," Michael sighed, pulling away.

“Keep dreaming!” John ground out, yanking on his chains again.

Michael turned away and retrieved something from a side table. It turned out to be another injected, which he administered despite John's protests.

“That should be the last one,” the mad scientist announced.

“I'm gonna kill you,” John growled.

"You'll never be able to go home," Michael said. "They'll never trust you again. I should find a mirror so you can see the changes. Change enough that you don't look entirely human anymore, John."

John closed his eyes, his mind calling all kinds of nightmare scenarios forward. He tugged on his chains, somewhat feebly.

“Just let me go,” he begged softly.

“No!” Michael snapped. “And don't ask that again!” The wraith-human hybrid sounded angrier than John had ever heard him. “You will come to care for me the way I do for you! I promise you that!”

John's eyes shot open and he glared daggers at Michael. “You don't tell me who I do and do not care for. I feel guilty for what we did to you, but I will never feel anything more than that for you.”

John's head snapped to the side when Michael suddenly slapped him so hard that he tasted blood. The room went quiet, Michael froze in shock for what he'd just done. John spit blood to the side, not at all fazed by the harsh treatment. He'd expected it.

“I'm sorry,” Michael whispered, still frozen in place. “I... I didn't mean to do that.”

“Oh, shut up,” John drawled. “It was going to happen sooner or later. Keeping me here against my will, locked in chains. The abuse was going to happen, whether you planned it or not.”

Michael stared at John blankly. The hybrid gulped quietly, then turned and walked out of the room. John glared at his back as he left, his mind weighing heavily on his situation.

Hours later, John was studying the parts of himself that he could see when he looked down. His arms were almost hairless now, the skin pale as death with a slight green tinge to it. His fingernails were longer and tougher and looked as though they'd been painted a gunmetal gray. He had one of those weird exoskeleton bone-like protrusions on his middle finger on either hand.

It was all too wraith-like. He was terrified to find out what his face looked like. So, of course, that's when Michael walked in, carrying an old hand-mirror. He didn't want to think about where he'd gotten it.

John watched him carefully, as Michael stood beside him and studied John's face silently.

“Would you care to see how beautiful you've become?” Michael asked, smirking.

“Not really,” John replied. “I'd like to know how to change back into the normal human I was before.”

“There is no going back,” Michael growled, setting the mirror aside. “You have no choice but to be what I have made you. You're mine now!”

“That's all this is, isn't it?!” John shouted. “Taking me out of the game. Making me your pawn instead of theirs!”

“You will never be a pawn, John Sheppard,” Michael said, his hand coming up to caress John's face. “You're going to be my queen.”

“Why?!” John snapped.

“Because I love you!” Michael snapped back, shocking himself. He froze for a moment, then brought both hands to John's face and smashed their lips together again.

John bit Michael's lip, but it didn't faze the obsessed hybrid. If anything, it just spurred him on. Michael moaned, his tongue making a bloody home for itself in John's mouth. John tried to turn his face away, but Michael's mouth was practically glued in place.

Suddenly, Michael's hands began tearing at John's clothes, ripping away his shirt completely. When his hands found John's belt and the placket of his pants, John started pulling frantically on his restraints. Michael seemed to ignore his distress.

The hybrid's hand found a grip on John's cock, the former human was relieved that he still had one. That didn't mean that he wanted Michael touching it.

Michael's lips trailed down John's jaw and neck. His teeth nipped at John's neck, licking at the taut tendon leading back up to his jaw.

“You taste amazing,” Michael panted, his voice tight with arousal.

“Get your damn hands off me!” John shouted. “Michael!”

The hybrid seemed to ignore his plea, continuing his exploration of John's body. He pulled back and John could see his pupil blown wide. Michael moved to undo the chains holding John's ankles down, then proceeded to pull at John's pants. He seemed deaf to John's shouts.

“No!” John gasped. “Stop!”

Michael tossed John's pants aside, along with his boots. He climbed up onto the table, forcing John's legs apart. John tried to kick him, to struggle as much as he possibly could, but Michael was much stronger than him.

“Don't do this!” John begged loudly, pulling violently on the chains holding his wrists to the table.

“You're making me do this,” Michael panted. “I need to prove to you that this is a good thing. Convince you that you're meant to be my mate. If you weren't, it wouldn't have been so easy to make you better.”

“This isn't better!” John growled, thrashing around.

Michael let his weight force him still. John could feel Michael's erection poking against his exposed and drastically changed body. Distantly, John realized he still had a penis and testicles, and most likely a prostate.

But there was also a new orifice, and Michael wasted no time to push his fingers into it. John froze up in shock and discomfort. The sensation was strange and something he never even dreamed he'd ever feel.

Michael really was going to make him have their children. Why was this happening to him?

The hybrid used his other hand to free his straining cock, making John's blood freeze in his veins.

This could not be happening!

“Michael, don't!” John yelled, but the hybrid seemed to be out of his mind with lust. “It's just the pheromones. You said so earlier. You don't want to do this!”

“Oh, but I do,” Michael gasped, stroking himself and rubbing his precum up and down his shaft. His other hand still playing with the newly formed opening in John's body.

“Michael!” John begged, trying desperately not to lose his mind in sheer terror. “Please don't!”

“I have to,” Michael groaned, laying himself out over John's body, forcing his mate to spread his legs further.

John could feel the head of Michael's cock pressing into the freakish new orifice. The Colonel began a mantra of 'no no no' again, while tears leaked from his eyes.

“You're so beautiful,” Michael whispered, as he pushed inside.

He breached John's body, violating a space he'd never thought he'd have.

John grit his teeth, holding in his breath as he was overtaken by pain. He didn't just grow girl parts, he grew virgin girl parts. He felt like he wanted to vomit, especially when Michael bottomed out and moaned into John's ear.

“Finally,” Michael gasped.

One hand grabbed the back of John's neck and forced him into another kiss, as he started bucking and grinding his hips slowly. He didn't want to rush. He wanted this first coupling to be as special as possible. It was already happening on a spur of the moment, he didn't want to devalue it by rushing.

Michael ground into John slowly, lips still sealed over his mate's. He groaned with every thrust, swallowing the whimpers John couldn't choke back.

John gave up on biting Michael's lips and tongue. He clenched his fists so tight his bones creaked. He was not enjoying this in the slightest. Now he understood why women had a harder time finishing than men did. It hurt!

John's obvious discomfort was not enough to stop Michael from picking up the pace until he was pounding into John's body faster and harder. At one point, John let a sob slip through his teeth but Michael took it as a sound of pleasure.

“Yes, that's it! Open up for me!” Michael said once he'd released John's mouth. He groaned and looked into John's eyes with almost crazed eyes of his own. Michael wracked John's body with every thrust.

John closed his eyes, wishing for this to end. But Michael's thrusts became even more painful as he moved faster still. The table was creaking from the violent motions.

It seemed like this was going to go on forever when John felt a warmth filling his insides as Michael gave a loud groan before he bit down on John's shoulder as a lay of claim.

Then everything stopped.

The only sound was their panting. Michael licked at the mark he'd left on John's body, lazily licking up the small amount of blood. He moved his lips up, kissing John's jaw and cheek, as the soldier lay listless under him. He brought his mouth up to John's ear and nuzzled into his hair.

“Now you truly are mine,” he said into John's ear. “My mate. You don't belong anywhere but with me.” John said nothing, just stared off into the distance. Michael watched John's face closely.

“I'll let you come to terms with your new reality in your own time,” Michael said. “Just as long as you know that you will never be going back to Atlantis. Or Earth for that matter.”

John's eyes finally found Michael's. “Go fuck yourself,” he said softly. He was still listless for the most part, only his eyes showed his fury.

Michael finally pulled out of John, the feeling of semen leaking out was immediate. “I'd rather not,” the hybrid answered with a smirk. He looked John in the eye. “They will never accept you back there.”

“Humans aren't like wraith,” John said. “They know me, and they know I'd never hurt them. My friends will find me, and I will go home.”

“Your confidence in them is nauseating,” Michael commented, finally adjusting his clothing back into place.

He picked up the hand-mirror and held it in front of John's face. John got his first look at what Michael turned him into. It wasn't as bad as John's over-active imagination had come up with.

His skin was the same on his face as it was on his arms and hands. He had vague impressions of the wraith nasal slits, his hair had gone salt and pepper gray. His eyes were the same hazel they'd always been but his pupils were slitted now.

He still looked like himself, but he was just different enough that he didn't look human anymore.

“You don't belong with them anymore,” Michael said.

To be continued.

**Notes for the Chapter:**

> If there are any hideous mistakes, please point them out to me!


	4. Cooperation

**Summary for the Chapter:**

> Wraith and humans must cooperate if they want John Sheppard back.

**Notes for the Chapter:**

> This one's pretty short, sorry.

Making You Better Chapter 4

Todd growled at the trigger-happy Satedan, who was pointing his gun in his face.

“Ronon!” Dr. Weir warned. “He's here to help us.”

“Never trust a wraith,” Ronon hissed.

“A good suggestion on most days,” Todd conceded. “But today is not one of those days.”

He turned to Weir, ignoring the ape for the moment. “I have some news on our hunt for the one who kidnapped John Sheppard.”

Weir moved forward and pushed Ronon's gun down. She then gave Todd her full attention. “Go ahead,” she said, earning a smirk from the wraith.

“I have spoken with some of our worshipers on a planet near the outer edge of this galaxy. They had been in contact with the half-breed you call Michael.”

“Did he take Colonel Sheppard?” Weir asked.

“From what I've heard, I believe so,” Todd answered. “Though, I'm not certain on where he's taken him. There are many planets near that planet of worshipers that he could have gone.”

“How many?” Weir asked, trying not to show her nervousness.

Todd shrugged, a human mannerism he's picked up from his many interactions with Sheppard. “At least twenty, but it shouldn't take long to narrow it down. We have a way of detecting other wraith, or almost wraith, that should make things easier.”

"Then I want you to take some of our people and equipment to help speed up the search and to be ready to mount an immediate rescue operation if need be," Weird ordered, making Todd grin. 

“Make sure Dr. Beckett is among them,” Todd said.

"Why?" Weir asked though she was planning to send Beckett anyway. 

“Because if Michael took him, we would assume it was for some experiment, not simply to torture or kill him,” Todd answered.

A somber air filled the room. Ronon looked like he wanted to kill something, as did Major Lorne look as though he would gladly go on a killing spree the moment their enemy was in sight.

The Major greatly respected and admired his commanding officer. The thought of someone doing experiments on him, hurting him, was enough to severely wear away his calm.

“I'd like to be part of the company, Ma'am,” Lorne requested of Weir.

“I was going to suggest just that, Major,” Weir answered with a smile. “I want both SGA teams 1 and 2 ready to go in thirty minutes. And bring some more marines with you. As many as you feel is necessary.”

“Yes, Ma'am,” Lorne responded, then turned and left Weir's office, Ronon following behind.

Weir turned her attention to Todd. “I'm going to have them take two Jumpers with as well.” She stood and watched the wraith for a moment. “I'm trusting you with my people and their lives. I know you have an understanding with Colonel Sheppard, and I hope that extends to the people he cares about,” she said, deadly serious. “What I mean to say is, don't let any of your brethren eat any of my people.”

Todd let out a scratchy laugh. “Worry not, Dr. Weir. I want to find John Sheppard as much as you do. I consider him an honorary brother. As does my crew. He saved my life, after all.”

“Good,” Weir said with a soft sigh.

Todd nodded sagely, then turned and left her office.

The wraith communicated telepathically with his hive, informing them of their impending visitors. He laid down the rules right away. Allow the humans to live comfortably on the ship, include their expertise and manpower in the search, and the ultimate rescue of John Sheppard. No harm is to come to these humans, unless in self-defense.

It wasn't long before both Jumpers were loaded up with Major Lorne's SGA 2 team, the remnants of SGA 1, plus Dr. Beckett and ten more marines. They made sure to load up enough food to last a few weeks, and enough ammo to last through a few firefights. They followed Todd's dart back to his hive and landed the Jumpers right next to all the darts in the dart bay. 

Ronon was understandably on edge, but his tension was beginning to affect everyone else. 

“Ronon, we may be on this hive for some time,” Teyla said softly, as they disembarked and were shown quarters they could use. “You need to calm down before you do something foolish.” 

“I hate working with wraith,” Ronon groused. 

“Then you must be civil,” Teyla told him. “And make sure you keep your gun set to stun,” she added with a grin.

Dr. Rodney McKay had ridden in the Jumper fairly quietly, but once he was on the hive, he commandeered several computer terminals, hooking up his Earth tech to the Wraith tech. He barked orders to wraith and human alike, taking over the search for John in the tech department.

“I need to know which planets John could be on. I can cross-reference with the Ancient database and, hopefully, narrow it down,” Rodney said loudly, all in one breath. One of Todd's scientists quietly supplied Rodney with the information he needed.

The wraith that John had dubbed 'Kenny' oversaw the integration of the human search efforts with that of the wraith. He was quite amused with Dr. McKay's antics.

Todd overheard all the comments and complaints from his crew through their telepathic link. He had to remind them why they were doing this. 

Some still didn't understand or approve of the amount of work and resources they were putting into finding one human, who was probably dead. Those wraith were mentally reprimanded and reminded of who their commander was.

They quieted for the most part, but they still complained about having to share their workspace with rowdy humans.

To be continued.


	5. Abuse

**Summary for the Chapter:**

> Michael's possessiveness makes itself apparent.

Making You Better Chapter 5

After he was finished, Michael simply chained John's ankles down once more and left him naked on the table, bruised and sore and covered in things he didn't want to think about.

He just laid there and thought about his situation. He didn't much like where that train of thought was going either. He knew his friends were looking for him, and he knew that if anyone could find him it was McKay and Todd. So if they were working together, he held out hope that he'd be rescued soon. But another part of him had done the math on the probability of them finding him with an entire galaxy to search, and his hope took a huge blow, so he resolved not to think about it anymore.

After a while, John swore that he could hear voices. It took him several hours to realize he was hearing them in his head. It dawned on him that he was developing the wraith telepathic abilities.

He couldn't quite make out any solid thoughts yet. There didn't seem to be much in the minds of Michael's 'children', his hybrids. The only thing that was really present in their minds was the need to obey orders.

John started focusing on probing the minds around him, it wasn't like he had anything better to do. When he was starting to get the hang of it, he came across a mind that was more than the others. More organized? More complex? And filled with ambition and pride and a sense of accomplishment. 

When John figured out that he was connecting with Michael, it was too late to back out without being noticed. Michael had sensed him and immediately headed straight for John, his mind filled with elation and triumph.

John hastily pulled back, his heart rate picking up in a slight panic. Less than a minute later, Michael burst into the room excitedly. He walked up to the left side of the table John was on. His hand found John's cheek instinctively, and John was noticing a pattern of behavior.

“Your mind has evolved more quickly than I thought it would,” Michael stated in amazement, excitement seeming to have stolen his breath away. “Your transformation is nearly complete.”

“Then let me off this table,” John demanded. “I'm sore and hungry and if I don't get out of this room, I'm going to lose that mind you've been trying so hard to augment.”

“Are you going to try to run?” Michael asked skeptically. 

“No,” John said after a moment of hesitation.

“Let me get you some clothes,” Michael said, leaving the room.

John sighed heavily, rattling his chains impatiently.

Michael was back a few minutes later. He set the clothes aside and moved to undo the chains, watching John carefully, as he unlocked the chains around his ankles first, then moved to his wrists and paused.

“If you try to run or cause trouble,” Michael warned. “I will punish you and lock you up again.”

“Fine,” John said.

Michael removed the chains from his wrists and helped him to sit up. John's muscles screamed, and he groaned as he sat up and swung his legs over the side of the table. Michael carefully removed the electrodes he'd attached to John, then stepped between the Atlantian's thighs. John immediately tensed up, as Michael took both of his hands in his own. He raised them to his mouth and he kissed the bruises and abrasions left on John's wrists by the harsh steel. 

The hybrid looked up into John's eyes as John remained silent. His gaze was filled with what looked like love, and something more troubling – obsession. That's what worried John the most.

Reaching behind him, Michael retrieved the clothes he'd found for John. They were SGC standard issue, and that bothered John more still. Where was Michael getting all these Earth supplies?

“Thank you,” John said hesitantly, deciding to worry about the issue later. Michael gave a vague smile and helped John to get dressed, even though John insisted he could do it himself. The hybrid's hands wandered as he slid the pants up to John's hips, and lowered the shirt over his chest. The Colonel decided to try to ignore the lack of undergarments.

Michael wrapped his arms around John's waist, once he was fully dressed and standing on his own two feet. He pulled his mate close and pressed his nose to John's neck, where scent glands were giving off pheromones. He pulled a deep inhale and sampled a taste of John's scent. John allowed it – for now. 

“You're perfect,” Michael breathed against John's throat, pressing his body closer. 

John froze when he felt Michael's erection pressing against his hip. He kissed John's neck, his arms tightening their embrace. John's hands pushed weakly at Michael's chest.

“Not now, Michael. I'm still sore from before,” John whispered.

But Michael didn't seem to hear him, because his hands went down and grabbed handfuls of John's perfect ass.

“Michael!” John begged, pushing against the hybrid to no avail. He only felt Michael grind against him, the hybrid seeming to be deaf to John's protests.

It had to be the pheromones Michael had mentioned because this happened every time he came close to John. 

“Michael!” John shouted. “Stop!”

Michael pushed John back against the edge of the table, his hands skimming up the back of John's shirt. He bit down on the join between John's neck and shoulder. John groaned in pain, biting his lip against the urge to make any louder sounds.

John's anger spiked and he put everything he had into pushing Michael back. The hybrid only stumbled back a few steps, bumping into a work station. Michael glared up at John angrily, barely contained rage in his gaze and stance. John realized that he could now smell Michael's anger.

“Not now,” John said with as much steel in his voice as he could muster.

Michael advanced on John in two large steps. He grabbed John by his shoulders in a bruising grip. He forced his lips against John's but John turned his face away. 

“No!” John snapped.

“You will not refuse me!” Michael shouted. “I warned you about trying to get away!”

“I'm not trying to get away! I just don't want you to fuck me again!” John growled.

“You don't get a choice!” Michael hissed.

He flipped John around and bent him over the table. John swung his arm backward and caught Michael in the ribs. However, it only seemed to antagonize him. Michael became rougher. He held John's wrists behind his back with one hand, the other yanking John's pants down to his knees.

Michael wasn't interested in the new organ this time. Without warning, he pushed two dry fingers into John's ass, forcing a shout of pain from the soldier. Michael growled with pleasure, as he bent over John's back to nibble at his mate's neck. 

“You didn't think I only wanted you for reproduction, did you?” Michael purred into John's ear. He wriggled his fingers around in John's body, John becoming slick with what he assumed was blood. “I want you for pleasure, too, John.”

He pulled his fingers out of John, brought them up to his mouth and licked them. He then reached down and pushed his barely wet fingers back in. The fingers scissored inside John, as the Colonel gritted his teeth against the pain.

Then Michael's fingers touched on something inside him. John shouted out in surprised pleasure, and Michael groaned in approval.

“Found your prostate,” the hybrid said.

Michael pulled his fingers out and replaced them with something much bigger. With one powerful thrust, he was as deep as he could get into John's warmth, blood easing his way. John could not stop the scream that sliced its way out of his throat.

Michael moaned loudly. "Yes!" he cried out. He stayed still for only a moment before he began fucking John hard and fast. 

John felt shame swell inside him as he felt his dick harden against his will from the assault on his prostate gland. Michael's cock dragged over it again and again. John felt the pain of something tear, the pain of it not being quite enough to dampen the pleasure he was feeling. As a result, he didn't control the unexpected moan that went with his sudden orgasm.

John was immediately disgusted with himself for feeling any pleasure at all with this violation, much less enough to cum. Michael laughed softly – feeling, smelling and loving John's release.

“I knew you wouldn't resist me forever,” Michael said, speeding up his jarring thrusts. It didn't take much more for John's tight body to bring Michael off. The hybrid came deep inside John, then slumped over his back, panting heavily.

“You were meant for me, John,” Michael sighed with satisfaction after this round with his new mate.

John didn't respond. He stayed silent, imagining all the ways he was going to maim Michael before he killed him after he figured out how to escape from here. 

Michael finally let go of John's wrists, then pulled himself out of John's body, tutting at the amount of blood coming out of him.

"If only you'd cooperated more," Michael chastised. "You wouldn't have had to experience this pain." The hybrid scientist moved away for a moment after he'd straightened his clothes. 

“Don't move,” he instructed, coming back with a tin of salve. “My own creation, meant to improve the healing process for my hybrids.” 

He gathered a generous amount of it onto his fingers and pushed it into John, who hissed at the cold texture. It stung John's insides, making him tense from the pain, which started to ease after a few moments. 

"Next time, you'll cooperate, won't you?" Michael asked though it sounded more like a command. 

He pulled John's pants back up after he was satisfied that he wouldn't bleed anymore. He adjusted John's clothes as he helped him to stand up again. 

John was a bit shaky and very sore. He didn't make eye contact with Michael, more than a little subdued. Michael took John's hand. “Come. Let me show you your new home.”

To be continued.


	6. Hope

Making You Better Chapter 6

“What is this planet?” Rodney asked, pointing at a dot on the fleshy wraith computer screen. “Why was it ruled out?”

“It is uninhabited,” Kenny, Todd's second-in-command, said.

“But it's in the Ancient database as an outpost,” Rodney argued. “A research outpost.”

“Why does that matter?” Kenny asked. “There have been no life signs on that planet for many years.”

“But we are looking for a crazy wraith hybrid, who is a scientist,” Rodney groused. “It would be the perfect place for him to do his crazy experiments. And when was the last time anyone checked that planet for life signs? If the answer isn't within the last few days, we should check it again.”

“That would take us out of our way and waste valuable time,” Kenny argued.

“Just check the damn planet!” Ronon growled from his place leaning against the wall, putting his hand on his gun.

Kenny hissed in irritation and looked toward Todd for his orders. Todd nodded at his second.

“If Dr. McKay thinks it is worthwhile, then we should check,” Todd said. “Leave no stone unturned.”

Kenny growled but turned to the navigation console and changed the ship's course.

John was shown around a facility that was definitely Ancient. All the lights and computers turned themselves on when John came close. Michael was grinning, obviously congratulating himself on his choice.

Finally, John was brought to a room that looked as though a Wraith hive ship had thrown up in it. There were all kinds of fleshy tubes and veins growing all over the walls. There was a bed in the middle of the room that looked like it had grown there like a fungus. The door seemed to be made of thick leathery skin, like bat wings. It snapped shut behind them like a muscle contracting. 

“This is where you will play a majority of your new role,” Michael drawled, a smirk on his face.

“Oh, will I, now?” John asked, voice dripping with sarcasm. 

“Yes,” Michael said simply, a minor challenge in his tone.

John turned to glare at him. “I'm not your slave, Michael.”

“No, you're my queen and my mate,” he replied.

“If I'm a queen shouldn't I be the one giving orders?” John asked.

"Eventually, yes," Michael said. "Once you've shown a willingness to preserve the hive, you will be given more responsibility. For now, though, you are simply tasked with increasing our numbers." 

John beat down the urge to punch something. Preferably Michael's face. Or his nuts. Either would suffice.

Apparently, John's mental imagery was strong enough to project, because the next thing he knew the room was filled with Michael's laughter. 

“So spirited, John,” the hybrid chuckled. “Queens don't get their hands dirty like that. They have drones do the dirty work.”

“Get me some drones, then!” John shot back. 

Michael simply smiled. “You have to birth them first,” he supplied.

Suddenly, John wanted to throw up. He vaguely realized that this situation was just nauseating all around, with how much his stomach was protesting. He could not believe Michael really wanted to make him the queen of a hive.

“That's a disgusting thought,” John replied, grimacing.

"It's an arousing thought," Michael mused, looking up and down John's body. "I would have you again right now if I didn't have other things to attend to." 

“Well, attend to them then,” John said snidely. “My ass can't take any more right now.”

Michael walked up to John and put his hands on his shoulders. He gently pushed John back toward the bed. “Sit.”

John narrowed his eyes but did as he was told. Which was a mistake.

The moment he sat down, several tentacle-like appendages shot out from under the bed and wrapped around John's wrists and up his arms. Another set wrapped around his ankles. He ended up spread-eagled across the bed. A few smaller tentacles crept down John's pants and into places they didn't belong. 

“What the fuck?!” John yelled.

“You need to rest and you need nutrients,” Michael said, watching John thrash around.

With that, another thinner tentacle slithered out and shoved its way down John's throat. He thrashed and struggled as much as he could, but the slimy appendages wouldn't give an inch. 

“Try not to struggle too much,” Michael commented, then turned and left John to this new nightmare.

It took them two days and several jumps through hyperspace to get to the planet's orbit. Rodney was extremely grumpy by then, knocking heads with Todd's crew members, whenever Rodney's own people couldn't stand him anymore. Which was often. Teyla tried to keep him fed and caffeinated to reduce his level of grumpiness, but it seemed a wasted effort. The longer they went without John there as a buffer, the more insufferable the scientist became. 

“No life signs,” Kenny reported with a smug triumph.

“But we're getting power readings,” Rodney countered. “Just in the one place that has to be the outpost.”

“Is it a ZPM?” Teyla asked.

“It could be, which means it could be shielding something,” Rodney said. “But an Ancient facility wouldn't stay powered up for no reason. A shield wouldn't stay up like that if there was nothing to shield. Ancient technology doesn't waste energy that way if there are no people around to use it. It basically puts itself into a kind of sleep mode when it's not being used. Nothing would be putting out power like that if it had just been left that way either. Unless it had been initialized by a gene carrier recently...” 

Rodney paused mid-rant and locked eyes with Teyla, who appeared to be thinking the same thing as him. Their eyes lit up with sudden hope.

“John,” she breathed.

Kenny was way ahead of them, informing his commander and the other Atlantians. Before long, the Jumpers were loaded up and several darts launched along with them.

Michael was interrupted from his exploration of his mate's body, which was still wrapped in many tentacles, by an urgent telepathic communication from his hybrids. They'd been found by a wraith hive ship. 

Michael shot up off the bed and was barely redressed before he was out the door that then sealed behind him.

Michael's first order of business was to find out whose hive was up there and send several of his children to get his hive back into the air. It had been hidden and shielded on the opposite side of the small planet.

When he finally found out whose hive it was, Michael saw red. Rage sliced through him like a hot knife. With the outpost initialized by John's presence, Michael was able to have Todd's darts shout out of the sky, but knew nothing about the cloaked Jumpers until the facility granted access to the recognized Ancient technology. The Jumpers were allowed to land inside the building through an access door in the roof.

No! He needed more time to get away. He was drowned by the instinct to take his mate to safety. Michael turned around and was going to head for John but he came face-to-face with the business end of a P90 and several angry Atlantians. 

"Where's Colonel Sheppard?" Major Lorne demanded, finger on the trigger. He was backed by Carson, Teyla, Rodney, Todd, and several other wraith and even more marines. 

Michael feigned surprise. “Why would I have him?”

“Don't play dumb! We know he's here!” Rodney shouted, patience shot from long days on a wraith hive ship. He had a life signs detector in one hand and a 9mm in the other.

Todd stepped forward, eyes hard with barely contained fury. “I can smell him on you,” he said with a sneer. “You've hurt him.”

Michael couldn't resist the grin that spread across his face. “Many times and in many ways.”

To be continued.

Yeah, I'm an asshole like that.


	7. Rescue

Making You Better Chapter 7

"You son of a bitch!" Rodney yelled, his face turning red with rage. He just barely stopped himself from shooting Michael point-blank. 

“I see you spend much of your time around John, Dr. McKay,” Michael drawled, smirking at Rodney.

“Where is he?! What have you done to him!?” Rodney said through grinding teeth.

“You wouldn't understand even if I explained it to you,” Michael dismissed. The hybrid sighed, glancing at each person in turn, counting the weapons pointed at him. “I won't give him back,” he growled, directing his gaze at Todd again.

"What have you done?" Todd asked with quiet seething anger. 

“I made him better,” Michael replied.

Todd tilted his head to the side, eyes locked on Michael. “Explain.”

“You can't undo it,” Michael hissed.

“We shall see,” Todd said. “Explain.”

Michael straightened his back. “I simply expanded on the Iratus RNA in his blood with a few wraith traits,” Michael said off-handed.

“Oh no,” Carson groaned, shoulders drooping. Michael smirked.

“Explain,” Todd demanded again with more venom. He was pretty sure he knew where this was going, but he wanted to hear it from Michael's mouth.

“He had everything he needed to become a queen among hybrids. He just needed a little help,” Michael said, shrugging.

“Don't you mean 'king'? He's a man,” Rodney said, confused.

“No, he means 'queen',” Todd said with barely controlled anger.

“Wait, what?” Lorne asked.

“There's no such thing as a king among wraith. The queen acts as the center of a hive mind and increases their numbers, much like a queen bee in a bee colony,” Carson explained softly for the benefit of those confused. “How did you do it?” he demanded of Michael.

“That would be giving away my secrets,” Michael chastised.

Todd roared angrily, as he grabbed Michael by the throat and shoved him against the wall. Michael managed to cough out a laugh as he smiled at Todd's reaction.

“I knew he was more to you than you let everyone believe,” Michael choked out, still smiling. “He's mine now.”

“You know nothing of John Sheppard,” Todd said with an amused scoff. “No one can own Sheppard. He'd never allow it.”

“I didn't give him a choice,” Michael coughed his response, antagonizing the wraith even though he was still strangling him.

Todd let up his hold on Michael but didn't let him go. “You will take us to John Sheppard and explain what you've done to him, so Dr. Beckett and I can fix it.”

“There's no undoing it,” Michael repeated. “He'll never be accepted among those humans again.”

“You don't know us very well, then,” Rodney said. “I don't care if he's male or female, if he's pink or green and slimy, he's still my best friend!”

“I won't give him back,” Michael spat. “I can't. He's my mate.”

Todd suddenly growled loudly and threw Michael against the wall hard, then punched him across the face. Michael fell to the floor coughing, spitting out greenish-black blood. 

“How dare you violate him in such a way!” Todd shouted in his multi-toned voice.

“I told you he was mine,” Michael laughed, his hybrid blood dripping down his chin. “You can't kill me, no matter how much you want to. You'd just kill him too.”

“I'm not sure I understand what's going on here,” Teyla said.

Lorne raised a hand to his communicator. “Go ahead.” After listening to whatever was said, the Major turned to Todd and their wraith and Atlantian companions. “Ronon and the others have found a door that seems to be covered in wraith organics. They can't get it open.”

Michael shot up from the floor and ran in the opposite direction while they were distracted and before anyone could react. Lorne aimed his P90 at his back, but Todd pushed the muzzle down before he could shoot.

“We can't kill him,” the wraith hissed, as Teyla took off after Michael. Todd and the others quickly followed suit.

“Watch out! Michael's coming your way!” Lorne yelled into his com. “Do not shoot. Repeat. Do not shoot!” After a moment, he added, “That means no blades either, Ronon.”

Michael heard the people chasing him and ran faster. He pulled a stunner from his belt and fired blindly behind him. He managed to stun a few wraith and marines but it didn't help much. Teyla was still catching up to him. 

He turned forward and put all his focus back into running to his mate. They would not take him away from him! 

Michael rounded a corner and fire his stunner at the humans outside the bedroom door. Most of them ran and took cover around nearby corners, the rest were hit by the stunner and went down.

Michael ran to the door, ducking blasts from Ronon's gun. The door opened as he got to it and whooshed shut behind him just before Ronon could follow him through. He went straight for John, who had his eyes closed. John had been fairly unresponsive since Michael had secured him to the bed. 

He could hear Ronon pounding on the door, between blasts from his energy weapon. It would take a while, but he would eventually get through that door.

Michael pulled the syringe loaded with sedatives that he'd been carrying around just in case John put up a fight or caused trouble. He was about to inject John when the door opened. Teyla ran in first. He'd keyed the door open only for those with both human and wraith DNA. He'd forgotten about Teyla's heritage.

Todd was in the room after her, a stunner in hand. He didn't bother with it, though. Todd threw himself at Michael, tackling him to the ground and forcing him to drop the needle. 

The wraith and wraith hybrid fought each other as Teyla went to John.

When she got a good look at the state her friend was in, the Athosian didn't know what to do. She didn't know how to get him free of all the tubes and what seemed to be tentacles.

Ronon pulled Todd off Michael, a little surprised by how mad the wraith was. Though, he could understand. He was pissed too. “How do we get him out of this?” he asked of the bloodied Michael.

“You don't,” Michael answered, then lunged for the needle he'd dropped.

Todd put a stop to that by stomping on Michael's hand hard enough to hear bone crunch. “Give the command to release him,” the wraith growled.

Meanwhile, Carson was examining what he could of John on the weird wraith bed. He was intrigued by the whole thing but also a bit disturbed by it. There were strange tentacles wrapped around John's naked body. There was one down his throat apparently feeding him nutrients and providing oxygen as well. Another was going between his legs and Carson had a decent guess as to the function of that one. 

The marines stood around, while Ronon steadily got angrier and angrier as they all took in the sight of their respected and beloved commanding officer. Their minds were blown at the changes that were made in such a short time. They noticed the greenish, deathly pale skin, the loss of body hair and the just noticeable wraith nasal slits.

Lorne dug out a foil thermal blanket from his pack and covered John's lower body with it.

By this time, Todd and Teyla had wrangled Michael into a set of cuffs, both of them being none too gentle. Not after what they've seen.

“I don't even know where to begin getting him out of this mess,” Carson said. “I could probably cut him out, but I don't know if that would hurt him or not.

“Give the command,” Todd hissed, giving Michael a shake. Michael simply smirked silently. “If you do not, I will assist Dr. Beckett in removing him the hard way,” the wraith said. “But I don't think you want to risk John getting hurt any more than we do. And we certainly won't be just leaving the two of you here. John Sheppard is leaving this place, one way or the other.”

Michael glared at Todd silently. A moment later, the tentacles retracted, releasing John's body. John inhaled loudly as the slimy appendage pulled out of his throat. John's eyes slid open and he looked around at all the people looking at him. His eyes glanced over Carson, Lorne, and Rodney, then they landed on Todd and Teyla and he finally sighed in relief. 

“Carson, please tell me you can fix me?” John begged his doctor, his voice scratchy from disuse and having the tentacle in it.

“I'm going to try my best, John,” Carson responded with a smile, happy that he seemed okay.

A snarling sound came from Michael and John froze after his flinched noticeably. Seeing this, Ronon turned his gun on the mad hybrid and stunned him. Todd let him fall to the floor limply. 

Rodney finally came forward, helping Carson to sit John up. He produced clean pants from his pack and handed them to John, who accepted them gratefully. They helped him to stand and pull them on. John tried not to look at anyone. He knew what he looked like now. 

Lorne took off his tack vest and shrugged out of his jacket, then handed it to his commanding officer, replacing his tack vest after. John took the jacket, looking the Major in the eye by accident, but all he saw was a relieved smile looking back at him.

"Good to see you again, Colonel," Lorne said while handing him his own sidearm. "There's still a bunch of those hybrids out there, so you'll need this. But you'd feel safer with it in your hand anyway." 

“Yes, I would,” John agreed, taking the Beretta from his second-in-command. He looked over at Todd, noticing the tension in the wraith's stance. “Todd. Is something wrong?”

Todd blinked, clearing his throat. “He wasn't exaggerating when he said he'd made you a queen.” He glanced at the other wraith who had followed them into the room. They couldn't seem to stand still, which was odd for wraith. “The pheromones are fairly potent.”

John paused, glancing around at the wraith in the room. “Am I gonna have a problem with you guys?”

“No,” Todd answered immediately. “We have control of ourselves than that.”

"You sure? Michael sure didn't," John asked, muttering the last part to himself. Carson heard him though, making a mental note about other possible trauma. 

“You are safe with us, John Sheppard,” Todd promised, nodding his head once.

“Can we get outta here, then?” John asked the room at large.

“Yes, sir,” Lorne said, leading the way out.

One of the bigger drone wraith slung Michael's limp body over his shoulder.

To be continued.

There is plenty more of this to come.


	8. News

Making You Better Chapter 8

After a slow journey through the outpost, which resulted in the deaths of most of Michael's hybrids, John and the rest were safe on Todd's hive. They'd made an attempt at shooting Michael's hive out of the sky, but it had escaped into hyperspace along with the few remaining hybrids on board. 

John was taken to the queen's chambers, at the behest of the wraith on board. Todd blamed that on the pheromones John was giving off. The smell of a queen was wreaking havoc with the wraith's instincts. After learning of Michael's crimes, the wraith on the hive had been all too happy to lock the hybrid up in the most uncomfortably small cell the hive ship had to offer.

Carson was currently taking blood samples from John and asking him some general questions. When Todd finally left the room, Carson sat beside John, who was sitting curled up in a ball, hugging his knees to his chest.

“John, I need to ask you some uncomfortable questions,” Carson said, fidgeting with a pair of exam gloves.

“Do you need to ask them now?” John asked, looking at the clean exam gloves. “I know what you want to know. I'm pretty sure you already know the answers to most of them.”

Carson sighed. “But I need to hear the answers in your words. Let's make it simpler and you just tell me what happened?” he asked.

“From start to finish? Or do you just want to know how many times Michael violated me?” John responded, anger bubbling under his tone. He wasn't angry at Carson, he was just angry at the situation as a whole. “Should I tell you that I now have female parts down there right behind my male ones?”

“Would you mind if I did an exam?” Carson asked. “I need to check you for injury. And I need to tell me if you're in any pain and where it hurts. It could help me understand how to fix this, John, or I wouldn't ask.”

John tensed up, curling up tighter and resting his chin on his knees. “Maybe not right this minute. Can I work up to it?”

“Okay,” Carson said, putting the gloves aside. “Will you at least tell me if he hurt you, beyond the obvious?”

“I'm fine, Carson,” John said, a sense of defeat settling over the room. “He's beaten my pride to a pulp, but otherwise, I'm okay.”

“I will want a more thorough check when we get back,” Carson informed. “I at least need to do a scan, John. Standard procedure.”

“Admit it, Carson,” John said with a wry smile. “You're just fascinated by this whole thing.”

Carson smiled back. “Maybe a little, but I am concerned about you as well, John. You're my friend and my patient.”

“Thank you, Carson,” John replied softly.

“We're all worried about you,” the doctor added.

Todd walked back into the room a few minutes later. John was still curled up on the bed and Carson was just keeping him company, at least until John was ready to let him do an examination.

“Michael is awake,” the wraith said, scorn coloring his voice.

John tensed. He was getting tired of reacting to Michael that way. The hybrid had really gotten under his skin and it was pissing him off. John silently fumed, while Todd watched him. 

“You've developed telepathic abilities,” Todd commented.

John looked at him a frown. “How do you know that?” he asked.

“I can feel you,” Todd said mildly.

John simply stared at the wraith for a long moment before looking away.

“Truly?” Carson asked John. “You can connect to the wraith telepathically?”

“Yeah,” John said. “I can poke around human brains too.”

Todd smiled. “Like a true queen,” he said, earning himself a glare from the former human.

“I'm a Lieutenant Colonel in the United States Air Force,” John growled. “I am not some wraith queen!”

They stared at one another for a silent moment; Todd smiling and John glaring venomously. 

"You don't have to go back to being a human, John," Todd offered. "The crew of this hive have already shown a preference for having you stay. It's not every day a new queen comes along." He only won a sharper glare from the man-turned-hermaphrodite. "Just an option," the wraith added. 

Carson looked back and forth between the two of them. “No one would begrudge you, if you wanted to stay here and not go through the long and likely painful process it's going to be to change you back, in as much as I'll be able to,” he said to John.

John glanced at them both. “I'm already pretty sure I want to go back to my job in Atlantis, but I'll think about it.”

Todd smiled wider. “Perhaps we should take this opportunity to show you what it would be like to be wraith queen?”

“You mean being served hand and foot? Sitting in my quarters bearing children, while everyone else lives full lives around me? Or worse, doing the work of a bureaucrat?” John ranted, voice steadily getting louder. “No thanks!”

“There's much more to it than that, Sheppard,” Todd said lightly.

“I'm sure,” John said sarcastically, glowering.

“Do you object to the idea of bearing wraith or hybrid children?” Todd asked, suddenly changing the subject.

“It's not exactly my life's ambition,” John drawled.

"Well, then I suggest you start thinking about what you would do in such a case," Todd advised. 

“Why?” John asked, frowning in confusion.

“Because you are with child,” Todd said, his face and voice losing any levity it may have had.

John's jaw dropped, as did Carson's.

“You can't know that!” John gasped, silently begging the wraith with his eyes to be kidding, to take it back.

“Your smell is reminiscent to that of a pregnant queen getting ready to lay her eggs,” Todd said. “There's something different about it, though. No doubt having to do with your human DNA.”

“Oh boy,” Carson breathed, just before John slumped sideways, unconscious.

To be continued.


	9. Past

Making You Better Chapter 9

Michael paced in his cell. His mind was filled with his mate and his hatred for those who were keeping them apart. There was no way he'd be able to live without him, now that he'd had a taste of him. He felt like he was going mad. The scientific side of his brain wondered at that. This was unlike typical human or wraith behavior. It's as though mixing the two species had created a whole new race with its own set of rules.

He glared at his guards, which included the human oaf, Ronon Dex. The Satedan stood with his back against the wall across from the cell, glaring back at him. He looked as though he wanted to kill Michael and was just waiting for an excuse to do so. Michael wished he'd try something, so he could escape and find his mate.

“Stop thinking about him,” Ronon growled, grinding his teeth angrily.

Michael stopped his pacing. “You do not tell me what to do,” he spat.

“I do if you're thinking about going anywhere near John Sheppard,” Ronon replied.

Michael snarled, stepping up to the door. “He's mine!”

Ronon shook his head. “No, he's not!” He was tempted to pull his gun and put an end to the hybrid, but he'd been warned by Todd that killing Michael could cause problems for Sheppard. “The moment Dr. Beckett tells me you aren't needed to keep John alive, I'm going to end you.”

“That's never going to happen,” Michael shook his head, smirking. “He'll die without me.”

“That won't be the case for much longer,” Todd said, coming down the hall to Michael's cell.

Michael's attention snapped to the wraith. “What do you mean?” he hissed.

“I'm going to change him back to a human, as much as is possible,” Todd answered. “Once he gives birth anyway.”

A heavy silence filled the air, Michael staring at Todd unblinkingly. “It worked,” Michael breathed. Todd watched him with his head tilted. “I must see him,” the hybrid growled. “Now!”

“No,” Todd responded lowly. “You won't be going near him ever again. I'll keep you alive as long as is needed to ensure John Sheppard's good health, but you will never lay eyes on him again.”

Michael roared, slamming his weight into the cell door, snarling and growling as Ronon pulled his gun and aimed it at him. Todd simply tilted his head the other way, pushing Ronon's gun down with his non-feeding hand.

“Your aggression is quite interesting,” Todd commented. “An adverse reaction to the mating of two hybrids, perhaps.”

“It doesn't matter!” Michael spat. “He's my mate!”

“So you keep informing us,” Todd drawled, amusement in his tone. “Dr. Beckett and I need to know what genes you altered and how.”

“I'm not going to help you change him back!” Michael hissed. “He's better now. Perfect!”

“He doesn't think so,” Todd replied. “He's much less outspoken than usual.” The wraith stepped up to the cell door. “I suppose that might have something to do with the process that impregnated Sheppard in the first place. I don't believe he would have consented to the act. Not with you.”

Ronon growled and re-aimed his gun at Michael. “I'm going to kill this asshole!”

Todd pushed Ronon's gun down again. “We can't do that just yet,” the wraith said, staring at Michael's seething face. “It'll take longer, but we'll undo what you did.

“Good luck with that,” Michael said, smirking.

John woke up suddenly, sitting shot upright so fast he felt disoriented and almost toppled over again. 

“Whoa, John!” Carson said, walking over to the bed and sitting beside John. “Take it slow, lad.”

Carson had Kenny retrieve most of the tools he needed to do his work and bring them into the queen's chambers – John's chambers. He didn't think John would like to wake up alone at the moment. Todd had commandeered most of the marines to help keep Michael corralled. Teyla was resting until it was her turn to take over watching over John, and Rodney was way too loud for his presence to be prescribed by any sane doctor.

“You're alright, John,” Carson soothed.

John took one look at Carson, then shot off the bed and ran for the wraith equivalent of a bathroom to empty his stomach of bile it only had to give.

“That'll be morning sickness, I expect,” Carson said, handing John a wet cloth to wipe his face. “I think it is anyway. I don't know for sure, all things considered.” When John was upright once more, the doctor got ready to brooch an uncomfortable subject. “Uh, John, there's a serious conversation I need to have with you. Before Todd gets back.”

“What?” John asked, wiping himself clean and moving to the weird sink thing to rinse his mouth out.

“I need to know if you actually want to... go through with this?” Carson asked hesitantly.

John stared at his friend and doctor for a few long moments. “I don't know,” John finally said. “Wait, why couldn't you talk about this with Todd here?”

"Well, apparently, wraith are very pro-life when it comes to wee baby wraith," Carson said. "But I think it's really up to you, John. It's your body and your life." 

John bit his lip. “I need to think about this. I mean I never planned for something like this, even when I was married and my wife would've been the one getting pregnant. The subject never really came up.” John frowned. “Unless my dad was in the room. Then it came up no matter how uncomfortable everyone else was.”

Carson gave a soft snort of amusement. "Okay," he said. "Just let me know what you decide. I can help you talk through it too if you like. Or would you prefer to talk to Teyla about it?" he added. "She can help you list the pros and cons. She might be better able to help you think it over, she's always been better at those kinds of conversations." 

“Yeah,” John said. “I don't know. I don't know what to do about any of this!”

Carson sighed and put his hand on John's shoulder as he guided him back to the bedroom. “Well, until you can come to a decision, I'm putting you on bed rest just to be sure no harm comes to you or the little one,” the doctor ordered.

“The little one,” John repeated dazedly, putting a hand to his belly. He sat on the bed, lost in thought. “How did this happen?”

“I hope you mean that rhetorically and haven't actually forgotten,” Carson said.

John gave a sad smile. “Oh, I remember,” he said. “I won't be forgetting that any time soon.”

“Do you want to tell me what happened in more detail?” Carson asked, sitting beside him.

“Not now,” John repeated his earlier answer.

Carson sighed through his nose. “You're going to have to talk about it at some point, John,” he said. “It's not healthy to keep it all bottled up, Colonel. Even if that's what the military taught you to do.”

“I don't know how to do anything else, Carson,” John said. “I was taught to keep things buried and out of the way. Can't follow orders or issue orders that won't get everyone killed, if you're too busy thinking about what some asshole did to try to break you.”

“You make it sound like you've been through this before, John,” Carson noted worriedly. “I know you've been captured and tortured before, but have you ever... been raped before?”

John stayed silent for several long moments, chewing on his bottom lip, which sort of answered Carson's question without words.

“Will you tell me who and when?” Carson asked softly.

John didn't answer and Carson sighed again. They sat in silence for several minutes.

“Kolya,” John finally said. “When he captured me and had Todd feed on me. In between the broadcasts... he...” John went silent. He swallowed dryly, looking at the floor. “Probably part of the reason why Todd is being so protective of me. He watched the whole thing.”

“Oh, John, why didn't you tell me?” Carson asked, feeling a little like he'd failed his friend. “Why didn't I see any signs of abuse during your physical when you got home?”

“When Todd restored my life, all my wounds healed,” John said, shrugging.

“Except the mental ones,” Carson argued. “Those don't just go away. No matter how much we wish they would.”

“I know, but I could have lost my job, Carson,” John said softly. “Kolya wasn't the first person to ever abuse me that way. There was a CO when I first joined the Air Force. He liked 'acquainting' himself with all the 'pretty ones', as he liked to say.”

“Did you report him?” Carson asked.

“No,” John said, looking at his friend. “One of the other guys tried. He never came back to the training facility, and the CO never left, either.”

“Oh, my god,” Carson lamented, rubbing a hand down his face.

“You get used to it after a while,” John said, shrugging.

“That's not something anyone should have to get used to!” Carson seethed, clearly angry for his friend and every other soldier that has had to suffer from corrupt and antiquated rules.

“No, it's not,” John put his hand on Carson's shoulder for a brief moment. “But sometimes you have no choice but to suck it up.”

“Do you remember this CO's name?” Carson asked. “I won't tell anyone who told me, but I can at least file a report of suspicion.”

“Nothing will come of it,” John said. “Besides the SGC wanting to know which of their officers may be compromised by past traumas. All it would take is some research into who was ever under that CO's command to put the pieces together. And I don't particularly want that shadow looming over me. That I'm a magnet for sexual abuse. Most people blame the victim when they find out someone has been repeatedly abused.”

Carson only sighed heavily, unable to argue with John's assessment. Most people were bigoted about abuse victims or were simply at a loss for how to interact with them once they learned of their past. So, if John didn't want to make a report, Carson had no choice but to respect his wishes. 

“Humans are such primitive things, aren't they?” Todd said from the doorway, scaring the piss out of both of them. Neither of them had heard him come in.

“Dammit, Todd! Don't do that!” John yelled, putting a hand to his chest.

Todd tilted his head. “I'm tempted to keep you from going back to those humans, John Sheppard.”

“Good thing it's not up to you,” John growled.

“It could be,” the wraith argued. “If the other wraith were to learn of the danger you'd be in if you go back to Atlantis, they would be all too happy to assist in making sure you never go back.”

“What? You gonna lock me up, like Michael?” John demanded.

“No,” Todd replied. “But I would send your human friends on their way in the Jumpers they came in.”

“I'll steal a dart,” John countered, standing up.

“Not if I lock out those with the Ancient gene from the controls,” Todd sent back.

“You can't keep me here!” John shouted. “I'm not a damn queen! I'm an Air Force officer!”

“You're much more than that, John Sheppard, and you have been for a long time,” Todd replied, rendering John temporarily speechless and infinitely frustrated.

"No, I'm not" John finally said. "I don't know where you got the idea that..." John suddenly clamped his hands over his ears and groaned, sinking to his knees. 

“John!” Carson was by John's side in an instant.

John groaned again and rocked back and forth, his breath shortening into pants of pain. He let out a whimper and finally collapsed sideways. Todd was there to catch him before he could hit the floor, wasting no time in lifting him into his arms and laying him on the bed. Carson brought out a stethoscope and one of the Ancient hand scanners. John barely seemed conscious, but he wasn't completely unconscious either.

“John, can you tell me what's wrong?” Carson asked, speaking loudly in an attempt to rouse his patient.

John whined, hands still clamped to his head. “Michael...” he was able to grunt, just before he lost consciousness.

To be continued.

You should be used to this by now.


	10. Talk

Making You Better Chapter 10

Todd latched onto John's utterance and used his telepathic abilities to see what was happening in John's head. Michael was attempting to take over John's mind, to find out if he was truly with child and to try to escape with John.

With a mental command, Todd had one of the wraith guards stun Michael. Once the hybrid was rendered unconscious, John went completely limp on the bed, his head leaning against Carson's thigh.

“What the bloody hell just happened!?” Carson exclaimed worriedly, picking up his stethoscope once more, as he began checking John's vitals, starting with simply checking his forehead for fever with his hand.

“Michael was attempting to take control of John Sheppard through his telepathy,” Todd said.

“We need to revert enough of his DNA to at least disrupt the telepathic abilities, or Michael's just going to keep taking advantage of it and try that again and again until he succeeds,” Carson said.

“That could put the young one in danger,” Todd growled.

“Not much point in preserving the fetus if John gets hurt or killed,” Carson argued. “Especially if Michael does try that again!”

Todd hissed at Carson, getting in the doctor's face. “We will wait until after the birth to make any alterations to Sheppard's body.”

“Why do you want John to have this baby so badly?!” Carson demanded. “He's not even sure he wants to keep it!”

“You asked him?” Todd hissed again, getting angrier and angrier.

“I'm his doctor and his friend, it's my job to ask him these things,” Carson shot back.

Todd seethed for a few silent moments. “Why is he unsure?” he asked hesitantly, taking a breath to calm himself.

“He was born a man, raised as a man, never had any gender identity crises that I know of. For him, having babies has always been a woman's job, not his,” Carson explained carefully. “Of course he's unsure if he wants to keep a child that he'll have to deliver and take care of. A child that's been forced on him. He'll have no idea how to raise it either, it's part wraith!”

“All the more reason for his to stay with us,” Todd reasoned finally.

“He doesn't want to stay here,” Carson reminded.

“I'm feeling more and more disinclined to allow him that choice,” Todd said lowly.

"You'll only push him away from you and this hive if you take his freedom from him," Carson said. "You'll be no better than Michael to him." 

Todd growled deep in his throat, reaching to brush his feeding hand over John's forehead before he stood and turned to leave. Carson only sighed behind him, as the door whooshed shut behind the wraith.

Michael woke up on the floor of his cell. He sat up and adjusted a crick in his neck before he stood and faced the door to see Todd standing there watching him. 

“You will never try that again,” Todd hissed softly.

“You have a way of stopping me?” Michael asked, tilting his head.

“No,” Todd answered.

“Well, then,” Michael said, leaving it hanging.

“I'm hoping that by informing you of the mental and physical distress John experienced when you tried to take over his mind, you will refrain without my needing to interfere,” Todd said.

“It would not have harmed him,” Michael replied. “A headache maybe, but nothing that would damage him.”

“If I have to keep you sedated, I will,” Todd warned. “You will never try that again.”

“I will find a way to escape, sooner or later,” Michael warned softly. “With John.”

Todd turned to Ronon, who was still on self-imposed guard duty and grinned at him.

“If he moves or blinks in a way you perceive as threatening or suspicious, shoot him,” Todd ordered joyfully.

Ronon liked the order given so much that he didn't feel the need to berate the wraith for ordering him around. 

“Absolutely,” Ronon said, pulling his gun and just waiting for Michael to move. He was even more pissed off after hearing what the hybrid had tried to do.

Michael stared at Ronon, as Todd took his leave. The hybrid curled his hands into angry fists and Ronon fired his stunner at Michael.

John woke again. He was getting pretty tired of waking up from bouts of syncope rather than from just falling asleep like a normal person.

Carson was gone but Teyla was sat beside him on the bed, gently running her fingers through his hair. She was humming some gentle song he'd never heard before. He assumed it was an Athosian thing.

“Hey, Teyla,” John sighed, his voice gravelly from sleep.

“John,” Teyla responded, ending her soft humming, but her fingers only pausing for a moment before she continued the soothing gesture. “How are you feeling?”

“Like I want to finally wake up from this nightmare and get up to work on mission reports and personnel evaluations,” he replied. “Never thought I'd ever miss paperwork.”

Teyla chuckled softly. “I'm afraid that is not possible. For all that you may wish this to be a dream, it is real.”

They were both silent for several long minutes, Teyla's fingers always stroking his hair. John contemplated his situation, wondering what would come along with having a half wraith baby.

He resituated himself until his head was on Teyla's lap. “What am I gonna do?” he asked softly, a weary groan in his voice.

"To figure that out, you must first ask yourself all the necessary questions," she replied. "Or at least the ones you want to be answered." Her hand switched from stroking his hair to brushing it back off his forehead so she could still see his eyes, even though they were closed. 

“Which are?” he asked.

“Well,” Teyla began. “Have you ever thought about having children?”

“Once in a while, I guess,” he replied honestly.

“Would you be willing and able to take care of a child that is of your own flesh and blood?”

"If I have to, yeah," he replied, frowning. "I've never really thought of what I'd do with my life outside of the military, so I don't think I'm exactly mentally prepared to raise a child, but if the situation were to arise – which it has – then I guess, I could probably just try my best." 

“Do you realize you have many friends who love you and will do everything in their power to help you and protect you and your child?” she asked, a smile in her voice.

John looked up at her. “Teyla, I look like a wraith and the baby will too. No one's going to trust me again, especially the SGC. I'll end up in Area 51 being experimented on.”

"I do not believe General O'Neill would allow that, nor would Dr. Weir," Teyla argued. "And if there is any perceived threat, the people of Athos would gladly keep you and protect you from any harm. I am fairly certain that Ronon will stay by your side and protect you if you need him to. Or even if you do not need him to." 

“I'm supposed to be the one doing the protecting,” John groused.

“For now, you will have to delegate your responsibilities to Major Lorne and Dr. McKay,” she said. “Rodney is quite distressed that we didn't find you before Michael completed his experiment.”

“It's not his fault,” John said. “Where is McKay anyway?”

“Working with Dr. Beckett and the wraith scientists of the hive to come up with something to help change you back to a normal human, or in as much as that is possible,” she said. “But Rodney is a little out of his depth in this instance. Shall I got get him so you may see him?”

John shook his head. “Not right now. He'll just get weird-ed out by my face.”

“John, you do not look so much like a wraith that we cannot see the human in you, and recognize you as our dear friend, John Sheppard,” Teyla said.

“My skin is so pale that I look like I'm dead,” John pointed out. “I have wraith nasal slits!”

“But you are still you,” Teyla argued. “We will accept you, and I know Atlantis will be pleased to have you back.”

“I miss Atlantis,” John sighed.

“We will be back there soon,” Teyla assured.

“Todd made it sound like I was never leaving this hive,” John informed.

“No one will keep you from going wherever you please. I will make certain of it,” she promised.

“Thanks, Teyla,” John replied, thankful for his friend's promises, but still doubtful that he'd ever make it home.

To be continued.  
Are you annoyed with me yet?


	11. Attempt

Making You Better Chapter 11

It was two days later that John was feeling stronger. Michael hadn't tried to mess with his head, owing to the fact that Ronon kept stunning him almost as soon as he woke up. At least until Ronon was forced to rest.

John was up and about the ship. All the wraith seemed eager to assist him or do things for him. It was really weirding him out.

Todd was mostly an ever-present fixture wherever John was, unless he was needed elsewhere. Carson and Kenny took turns playing John's doctor because Carson couldn't be on-call twenty-four seven. 

Kenny had just finished examining John with a wraith medical scanner when a drone suddenly burst into the room and stunned Todd's second-in-command.

“What the hell?!” John yelled, standing up.

He tried to back away but the drone grabbed John by his scruff and slung him over his shoulder. John struggled fruitlessly, yelling as the drone raced through the corridors. It stunned everyone they met on the way to the dart bay.

John kicked and screamed against the giant bulk of the over-sized drone. “Let me go, goddammit!”

The drone wraith took every blow John delivered in his struggles as though they were mere mosquito bites. A normal person would have been taken down by them many times over, but the wraith was like a brick wall.

He fought until he was finally lowered into another set of strong arms. He was turned around and pushed up against a wall, he got a look at his captor and was unsurprised.

“Michael,” John gasped, renewing his struggles, attempting to throw his elbows into any part of the hybrid he could but Michael had a hold of his wrists. He hated how much stronger this hybrid was than he was.

The look on Michael's face was one of relief and rage. “Now we'll be leaving,” Michael said, dragging John away by his wrists.

"No!" John shouted, trying to shout loud enough to be heard by someone, anyone. He dragged his feet, but Michael seemed to have little trouble like he was an adult dragging along a crying toddler. “Let me go, Michael!”

He watched at the drone wraith raised his stunner and aimed it at John. Obviously, Michael had control of this drone. Before the drone could fire, a stunner blast hit the drone in the back. John saw Ronon running furiously toward them.

Michael tried to continue dragging John away, but John dug his standard-issue boot heels in, trying to pry his wrists out of the hybrid's grip.

“You're coming with me!” Michael growled, yanking John's arms violently.

They were only a few feet away from the nearest dart when two stunners hit Michael and John fell back onto his ass, as Michael hit the ground. Before John could even think about getting up, he was lifted into Todd's capable arms. 

The wraith commander silently carried John back to the queen's quarters and placed him gently on the bed. He took John's hands carefully into his own and examined his already bruising wrists. Todd sighed as he observed the damage. Carson was there a minute later.

“I wish Michael had given you the ability to feed,” Todd hissed.

John's eyes snapped up to Todd's. “Even if I could, I wouldn't do it!” he spat.

“Queens should never be marked in such a way,” Todd said, ignoring what John said. “You need to heal.”

"Not at the expense of someone else's life!" John said as Carson wrapped freshly cracked emergency ice-packs around his wrists, fixing them in place with ace bandages. 

“The drone who was weak enough to be manipulated by the hybrid would make the perfect sacrifice,” Todd continued.

“You can't just kill the drone because Michael is an asshole!” John argued.

Todd left the room without another word.

“Todd!” John yelled after him, but he knew he wouldn't listen. He wouldn't be able to stop Todd from doing what he thought necessary.

“That was a close call, John,” Carson said. “I know Todd and his crew want you here, but I'd say the sooner we get you back to Atlantis the better.”

“Yeah,” John sighed in agreement. “I don't think it's gonna be that easy, though. Todd's acting weird. Normally, he's more flippant with me, but now he's being serious and showing a level of emotion I didn't know wraith could feel. And, somehow, he's got his whole crew feeling the same way. It's freakin' me out!”

The withered husk of the drone's body dropped to the floor in front of Michael's cell, where the hybrid had finally woken up. Michael simply raised an eyebrow at Todd, whose face was expressionless.

“A sacrifice made to heal the damage you've done,” Todd said with a hiss. “You hurt him again. How many times must he suffer, Michael?”

"He wouldn't need to suffer at all if he were to leave with me right now," Michael replied. 

“That is never going to happen,” Todd said, turning to leave. “I must go heal the queen you've created.”

“So you do view him as a queen,” Michael observed. “I would have thought you would think him unclean, the way wraith view me.” 

Todd turned back to Michael. "The brothers of this hive are not so narrow-minded as to turn our noses up at an oddity with such potential. We endeavor to change ourselves so we may do away with the need to feed. Who are we to turn away someone who is the personification of what we wish to be," Todd replied. "No matter how his physiology came about. He is one of us." 

“But he feels like a queen, yes?” Michael pressed.

“Yes, however you made that so,” Todd said. “It doesn't matter. He won't be a queen for very much longer. As soon as he gives birth, he wishes to become as human as possible.”

“You can't undo my work!” Michael snapped. “It would kill him.”

“It's his choice,” Todd said.

Michael growled at Todd, stepping up to the cell door. “Give me my mate!”

Todd turned and walked away, smirking to himself when he heard Michael begin to scream and rave in his cell.

To be continued.

I know this must be frustrating, but comments do make me work faster! *grin*


	12. Assault

Making You Batter Chapter 12

Todd walked back into the queen's chambers about ten minutes later. 

“He insists on calling you his mate,” the wraith hissed, as he walked over to John, who was laying back on the bed. “I must heal you.”

“They're just bruises, Todd, you don't need to heal them. They'll be gone in a few days,” John shrugged.

Todd quickly advanced up to the bedside, shoving Carson aside – who squeaked with indignation and kneeled up on the bed. "You'll need all the strength you can get. Don't struggle." 

John struggled. “Don't!” He struggled as Todd yanked his shirt open and put his feeding hand to John's bare sternum. John gasped and stiffened as life was forced into his body, his struggling slowed as his breathing sped up.

Carson stood off to the side, shaking his head. The wraith was really going to push John away if he didn't stop making the Colonel's decisions for him.

John groaned as he felt his bruises heal, as well as the wound from the contact with Todd's feeding hand. Todd finally pulled away, after a long silent minute of pushing life into John Sheppard's body. John took a few moments to collect himself before he glared at the wraith venomously. 

Todd really should have seen it coming, but apparently, he didn't. The next moment, John's fist collided with Todd's cheekbone and sent the wraith tumbling to the floor. 

“I said I didn't want you to do that!” John shouted, his irritation only growing when his split knuckles healed immediately. He shot up off the bed, despite Carson's weak protests. His irritation only rose further when Todd stood up without even a scratch on his face.

“It needed to be done,” Todd reasoned.

“No, it didn't!” John growled through his teeth. “They were just bruises, Todd! I've dealt with much worse injuries than that without a wraith shoving someone else's life force into my body!”

“You need to stop thinking like a human!” Todd hissed.

“And why the hell should I do that?!” John snapped.

“Because you aren't one anymore!” Todd yelled back.

Silence rang through the room.

“Get out,” John said softly. When Todd made no move to leave, John picked up the closest thing to him, which was Carson's tablet – unfortunately, and flung it at Todd's head. Todd ducked easily, allowing the piece of Earth tech to careen over his head and crash into the wall. “Get the hell out!” he shouted.

Todd wisely retreated, as did Carson. Once out the door, the doctor turned to the thick-headed wraith. 

“I warned you,” Carson said softly, then turned and walked away.

Todd growled and stomped off in the other direction.

It was only the next day when the shit hit the fan again.

John was hiding in the dart bay, in the pilot's seat of Jumper One. Well, he was pretending that he was hiding, he was pretty sure most of the crew of the hive knew where he was, as did Lorne.

As an extension of Atlantis, the Jumper had a telepathic connection to John. She was practically singing to him. Atlantis didn't care if he was part wraith or part bug. To her, he was still John Sheppard, the human closest to being an Ancient. The Jumper was almost begging him to go flying. He would have loved to go, to just fly away, but he knew he'd be brought back kicking and screaming – if not by his fellow Atlantians, then definitely by Todd.

John fiddled with the controls, playing with settings, wondering if he should run a flight simulation just for the hell of it.

He sighed when he heard someone walk up the ramp of the Jumper. So much for hiding. He turned in his seat and froze, as he came face to face with Michael, who was armed with a stunner and a Beretta.

Suddenly worried that Michael may have killed someone, John shot out of the seat, intending to try and disarm the hybrid. 

Michael leveled the stunner at John's chest. “Sit,” he ordered. John sat down slowly. “Good, you can fly us out of here.” Michael reached out and pressed the button that closes the rear hatch.

John shook his head. “I'm not flying us anywhere, and you can't operate a Jumper without me.”

Michael sighed softly. “Don't make me do things the hard way, John.”

“Not gonna make it easy for you either,” John replied.

Michael kept his eyes on John, as he put the stunner and the handgun down on one of the back benches. He stepped forward and grabbed John's face in both hands, a gesture he seemed to enjoy doing, and crashed his lips against John's.

John tried to pull away before Michael's lips could make contact, but he wasn't fast enough. He used his position in the seat as leverage to push Michael, just as the hybrid tried to push his tongue in.

Michael fell back against the wall, but it didn't seem to faze him. He straightened back up, an almost manic grin spreading across his face. John saw the glint in Michael's eyes, as his pupils dilated, then he looked down and saw the bulge in the hybrid's pants grow bigger.

“Oh crap,” John muttered. He knew that look on Michael's face, it always preceded a sexual encounter with the hybrid. John's weird pheromones driving the man crazy with lust every time. It was like Michael went into a rut every time he was near John.

John made a move to reach for the lever to the rear hatch but Michael grabbed him around the middle and hauled him to the floor in the front compartment. John hit the floor with a loud and painful clatter. He kicked his knees up, hoping to hit Michael in a sensitive area, while the hybrid wrangled John's flailing arms.

“You will not resist me!” Michael growled, finally pinning John down with his body halfway leaning against the wall. Michael was planted between John's thighs, the hybrid using his advantage to hold John's arms pinned to the wall above his head with one hand.

They were both panting from the exertion by the time Michael was done wrestling John down. John glared up at Michael furiously.

“Go to hell,” John hissed, still wriggling around under the hybrid's weight.

Michael said nothing, silently leaning in to lap at John's throat, then he bit down and sucked a dark bruise into it. As he did that, he used one hand to pull at John's pants, yanking them down his thighs. He lifted his mate's hips and put his bare ass into his lap.

“No!” John growled, his teeth clenched. He tried to pull his wrists free of Michael's grip, getting the back of Michael's hand across his face for his efforts.

Michael pressed his weight into John to hold still, as he fumbled with his leather pants to free his throbbing erection.

“Stop!” John yelled, just as Michael pushed into John's female organ hard enough to hurt. John's whole body tensed up, his jaw clenching shut in discomfort. “Michael...” he whimpered. The wraith hybrid didn't bother with any kind of foreplay or preparation. Pleasure didn't seem to be part of his agenda, as he pounded in and out of John's unwilling body at a punishing pace.

Michael growled in his throat, biting down on John's neck again. He gripped John's wrists tight enough to bruise, as he plowed his mate into the wall.

John stopped calling out vocally, but neither of them realized that John was practically screaming in his head and that of the hive mind. 

A very pissed off Todd with a team of seething marines were on their way to the dart bay.

Not knowing this, Michael continued his assault on John's body. He was totally unaware of everything but having his mate under him again, being inside him again after days of going without.

Tears gathered in John's eyes after Michael's teeth broke through skin. He felt Michael's release into his body moments before he heard the rear hatch hiss open. Seconds later, the hybrid was ripped away from John by Todd, who threw him to the marines. They were none too gentle as they stunned him and dragged him away. 

Todd watched them take Michael away, then stared down at the trembling form of John Sheppard. His fury rose to a boil when he had to help the newly-minted queen right his clothing.

“I'm going to kill him,” Todd growled in his multi-toned voice.

“Get in line,” Lorne said from beside them. John curled up against the wall, wrapping his arms around his knees. The sight of the dimming light in his CO's eyes angering the Major. “It can't go on like this. Constantly watching and waiting for Michael to take over someone's mind, without knowing who he'll compromise in the process, just so he can attempt to kidnap Sheppard again." 

“I will keep the half-breed sedated,” Todd said.

“That's not good enough,” Lorne replied, as Carson finally raced into the Jumper. “No more dawdling. We're going back to Atlantis as fast as this thing will fly. He's not safe here.”

“And if we don't?” Todd challenged.

“I'd rather not go there,” Lorne replied. “He'll be safer in Atlantis, you can't argue with that.”

“'He' is right here,” John said softly from the seat that Carson had coaxed him into.

They were all silent for several long moments.

“Where would you rather be, John?” Lorne asked, losing the formality for this conversation. “On this hive, on Atlantis? On Earth?” He added the last as a passing suggestion, but it had Todd immediately on edge.

At this rate, the wraith was going to have an aneurysm. 

John was quiet, staring at the floor. Carson tutted over the state of him but waited for his friend to make up his mind on his own. 

“Atlantis,” the Colonel finally said. “I miss my city.”

Todd silently stomped out of the Jumper in a whirl of leather. He reluctantly relayed the command to put the hive on a direct course for Atlantis. He felt an echoing disappointment coming from his crew.

“He wants me to stay here and be their new queen,” John said, watching the wraith walk away.

“Why?” Lorne asked.

“I honestly don't know,” John said.

“Right, well, at least we should get you back to bed,” Carson interrupted. “You've been through another traumatic event and you've been hurt again. You need to heal. The normal way.”

“Okay,” John agreed softly, moving to stand up. When he winced, Lorne went to help him stand and walk out of the Jumper.

For all that John would've loved to stay connected to the little piece of Atlantis, it was not conducive to rest.

To be continued.  
There's a taste of what you came for!


	13. Exam

Making You Better Chapter 13

Teyla met them on the way to the queen's quarters – John's quarters. “John!” she said, catching up to them. “You are alright?”

“Yeah,” John said at the same time Lorne said, “No.”

Teyla sighed. “Ronon has put himself on self-imposed prisoner guard duty again, even though the wraith have dosed Michael with a strong sedative.”

They made it back to John's quarters and Carson stopped Lorne and Teyla from following them in. “Nope, sorry,” he said. “I need to examine his injuries, so off you go!”

Teyla hesitated for a moment, understanding coloring her face. She took a page from her Earth friends and gave John a one-armed hug, instead of her normal show of affection. She gave Carson a nod and pulled Lorne out to stand guard outside John's door.

John trudged over and sat heavily onto the bed, a deep sigh rushing past his lips, as he winced spectacularly. His sigh turned into a groan of discomfort.

“Do you mind if I do an exam, John?” Carson asked carefully, knowing he had to tread lightly with this fresh assault. “I'd like to make sure he didn't do any real damage.”

“It's okay, Carson. You don't have to treat me like glass,” John said, trying for his usual flippancy.

“I just want you to be sure,” Carson said, coming over with exam gloves in hand. “I don't want to add to the feeling of violation.”

John bit his lip, then slowly started removing his clothing. “I'll be fine, Carson.”

“Of course you will, Colonel,” the doctor readily agreed, hoping the reference to his friend's rank might give him a semblance of strength.

John paused when he got to his pants. He was reminded why they weren't quite sitting right on his hips, from when Todd had hastily helped him pull them back up. He flashed back to having them yanked down by a monster he was irrevocably tied to.

Todd hadn't exactly explained what he meant when he told him that Michael had mated him, which apparently wasn't just sex.

“Do you need some help, John?” Carson asked softly, causing John to jump, still managing to startle his patient and friend despite his attempt not to.

“No,” John said stubbornly. He shoved his pants down and kicked them off along with his boxers, which were dirty with things he didn't want to think about.

Carson snapped his gloves on, transitioning to his clinical voice. “I need you to sit your bottom on the very edge of the bed and then lie back. Put your heels on the edge and just let your legs fall open.”

John did as he was told, trying to keep his breathing under control, as he felt the start of a panic attack tightening up his shoulders. His anxiety ratcheted up when he finally exposed his vulnerable parts to Carson. It was only his absolute trust in the doctor that kept John from snapping his legs shut and cowering away.

Carson carefully put his hands on the insides of John's thighs, observing the trauma to the outside first. “Right, you've got some rather definite bruising, which will be uncomfortable for a while. I'm going to move on to the internal exam now.”

With lubricated fingers, Carson pressed gently into John's new unwanted parts. “Some bleeding and tearing just inside there. He wasn't gentle, was he?” Carson asked rhetorically. 

"No," John answered anyway. "He really wasn't. He's like a mad man every time he comes near me. Todd and Michael have both mentioned pheromones. Obviously, they don't affect normal wraith as much as they affect the hybrid version." 

“Interesting,” Carson commented contemplatively. “Maybe there's some way I can at least neutralize the pheromones. I'll see what I can do. Now then, I need to check on the little one. Michael was rough with you, which means that little baby inside you felt every blow you did.”

“Okay,” John said uncomfortably, getting pissed at the sudden feeling of protectiveness that swept through him. He pushed his feelings down and resituated so the doctor could run a scan on him.

After a few silent moments of Carson running a small wand over his abdomen with a concerned look on his face, John finally broke the silence. “What's wrong?” he asked, fidgeting with the blanket on the bed.

“John, did you fall on your back at all during the ordeal?” Carson asked.

"Yes, Michael practically body-slammed me onto the Jumper floor," John answered. 

“You've got some internal injuries. Nothing too serious, mind you,” Carson said. “But definitely enough to make a normal pregnancy difficult. I don't really know what that means for you. I don't know how your body will handle this.”

“What kind of injuries are we talking about here?” John asked, sitting up and reaching for his clothes.

Carson helped John redress, then gently guided him to lay back down on the bed. “I'm putting you on immediate bed rest, John.”

“What's wrong?” John asked again more urgently.

“There's some bruising on your spine and kidneys. A few bruised ribs. It's minor. You probably don't even really feel any of it beyond a bit of soreness. Compared to some of your past experiences, it's almost nothing,” Carson replied. “Most concerning is a slight placental abruption.” 

“What does that mean?” John asked, his hand unconsciously going to his belly.

"It means part of the placenta has pulled away from the uterine wall," Carson explained. "If you get hurt again or strain yourself, you could have a miscarriage. That is if you wish to keep it?" 

John didn't answer, suddenly faced with the dilemma of losing something he didn't even ask for but had anyway.

“There is danger to yourself as well,” Carson continued. “If the abruption gets worse, you could bleed internally.”

“Bleed from what?” Todd asked from the doorway, having just walked in.

Carson turned and sighed, as John curled up under the blanket. “Michael was overly rough with John, too much so for the baby's health. The injury is such that any further rough treatment could risk both the baby's and John's lives.”

A slow deep growl started in Todd's throat. “It was one of your marines who was weak this time. Perhaps he should be the one to pay the price for your recovery.”

“No!” John yelled, sitting up and ignoring Carson's tutting. “I didn't even want you to do that to the wraith that he manipulated, why the hell would I let you go anywhere near one of my men?! Stay the hell away from him!”

Todd growled loudly, causing Carson to put himself between the two of them. “John, you need to lie back and calm down,” he said, helping his patient to lay back down. Then he turned to Todd. “As for you, there's every likelihood that John will heal just fine on his own, but it's not going to happen if you keep upsetting him and getting his blood pressure up!”

Carson shooed Todd out the door, telling Lorne about the threat to the poor marine who got mind-controlled by Michael.

Then Carson was back with John, letting the Major and Teyla deal with the angry wraith.

“We're only five hours away from Atlantis,” Rodney reported, as he finally visited John in the queen's quarters two days later.

Michael had taken John so far out into the boonies of the Pegasus galaxy, that it even took a wraith hive ship several non-stop days of multiple hyperspace jumps to get back to civilization.

“Good,” John said, nodding from where he was on the bed. “I want a real shower so bad, you couldn't even imagine!”

“I can guess,” Rodney said, smirking. “So, how is the little guy?”

"Fine, as long as I don't do a lot of moving," John said. "Michael, the asshole, did a real number on me. Even the wraith part of me is having a hard time putting things to rights. And Todd keeps threatening to force-feed me someone's life to make me heal faster." 

“Well, whose life would he give you?” Rodney asked, frowning. “There aren't any people on board for them to feed from, except us.”

“Yeah, I've had to argue with him about threatening your lives,” John supplied.

“Well, that's... disconcerting,” Rodney responded.

“Yeah, so, the sooner we get back to Atlantis, the better,” John groused.

“We're almost there,” Rodney said, smiling. “In fact, we should be close enough to establish radio contact very soon. Elizabeth will be happy to hear your voice.”

"It'll be nice to hear hers," John said, smiling. He was about to say something else until Todd walked in. John frowned, not wanting to argue with the wraith about something else. 

“I'm here to heal your wounds,” Todd announced, raising a hand to forestall John's no doubt scathing reply. “Before you get upset, you'll be happy to know that no one died to supply the necessary energy. Each member of the crew has volunteered to share small amounts of their own lives to achieve this.”

“Boy, you guys really know how to butter a man up,” John said sarcastically. “Why are your crew members so ready to do something like this for me?”

“I have already informed you of our desire to serve a new queen, especially one who is not like all the others. Your genetics would provide this hive with the changes we so desire,” Todd explained. “Our reasoning remains the same,” Todd said, stepping closer to the bed, raising his feeding hand. “Please allow me to heal your injuries.”

John glared at Todd, then finally sighed heavily. “Fine.”

Rodney moved aside with a weird squeak and clutched his tablet to his chest, as Todd kneeled on the bed. The wraith made a soft purring sound as he moved John's shirt collar down out of the way and laid his hand on the former human's chest.

John hissed through his teeth as he felt Todd's 'mouth' latch onto him. The next thing he knew was a wave of pleasure. He threw his head back and uttered a sound that was like a cross between a moan and a shout. John writhed on the bed, Todd purring louder, which all made poor Rodney extremely uncomfortable. He felt like he was watching something he shouldn't be.

“That's just... not right,” Rodney whispered to himself.

Todd hissed in Rodney's general direction, which had the scientist fleeing the room with another weird squeak followed by soft grumbling to himself.

It seemed like forever and only a fleeting moment before Todd finished feeding John's body the energy it needed and pulled his hand away. John panted as though he'd just run a marathon. Todd moved to stand beside the bed.

“Thank you,” Todd said. “It was causing us some distress to work with the knowledge that you were unwell.”

John grimaced, sitting up in the bed. “Well, thank you for figuring out a way to heal me without killing someone.”

“It was my pleasure,” Todd replied, bowing slightly. The wraith looked over to the door McKay had fled through, then turned back to John. “I will not get another opportunity to once again ask you to please stay with this hive.”

“I can't stay here, Todd,” John said, a note of pleading in his voice, wishing for the wraith to understand.

Todd sighed softly. “Then my hive may end up staying in orbit for a while.”

“Why?” John asked.

“If for no other reason than to study Michael's research, and to collaborate with Dr. Beckett on the process of returning you to your former glory after you've had your child,” Todd explained.

“So sure I'm going to go through with this having a baby thing,” John commented.

“I believe you are not the type of person to condemn a child, for any reason,” Todd said. “And, if you truly want nothing to do with the wraithling after its birth, we would gladly look after it in your stead.”

“Wraithling,” John repeated.

“It is what we call all of our immature offspring,” Todd provided.

John nodded. “I'll think about it, Todd. Michael said this pregnancy would probably happen like a human's, that means I've still got plenty of time to figure things out. And, if you guys want to hang around, then Atlantis might even be glad to have your help with a few things,” John smiled at Todd, getting an answering smile from the wraith, though it was a pretty creepy one with his sharp teeth.

To be continued.

I really need a beta for this shit!


	14. Home

**Notes for the Chapter:**

> Special thanks to Eos1969 for being my new beta!

Making You Better Chapter 14

“Atlantis, this is Major Lorne. Do you copy?” Lorne said into his earpiece as they got close enough to the planet. The wraith's sensors had picked up on the presence of the Daedalus in orbit as well. 

“Lorne, this is Weir. It's good to hear your voice,” Elizabeth responded. “We were beginning to worry. How did the search go?”

“We found Colonel Sheppard,” Lorne reported with a smile on his face and in his voice. There were some soft whoops to be heard over the radio from Atlantis. “There are some details that can't be shared over the radio. But I can let you speak to the man himself.”

With that prompt, John pressed the earpiece in his ear. “Atlantis, this is Sheppard,” he said, which was met by more, louder whooping and clapping on the other end.

“John!” Elizabeth said with a sigh of relief. “Oh my god, are you okay?”

“Um,” John paused, hesitating. “We'll decide the definition of 'okay' when you've seen me.”

“What does that mean, Colonel?” Caldwell's voice was heard over the air.

“It means I was the reluctant guest of a mad scientist for, apparently, over a month,” John said, voice dripping with sarcasm. “What do you think it means?”

“I think it means you could be compromised, Sheppard,” Caldwell commented.

John growled softly to himself. “We'll decide what 'compromised' means when you've seen me, too. Right now, I just want to be back in my city with my friends, eat some real food, and sleep in my own bed. Can I do that without having you up my ass the second I get there?”

“Yes, John, you can,” Elizabeth answered before Caldwell could.

“Thank you,” John sighed. “I will give you a heads up, though.” He paused for a very long moment, hesitating again, causing Elizabeth to prompt him into continuing.

“John?” she asked.

“I don't really... look like myself, at the moment,” John said. “But Carson says he can undo Michael's handiwork. Well, most of it.”

“What kind of handiwork?” Caldwell asked.

“Please refer back to the response to your last comment, Stephen!” John snapped. “I've been at Michael's mercy! You know, the crazy wraith hybrid with a bad habit of experimenting on people?”

“Don't argue, gentlemen,” Elizabeth interrupted. “Let's just be glad that John's back and in one piece.”

John's reception was met with mixed feelings and reactions. Most were glad he was home safe, but a few shied away as he was walked to the infirmary by an entourage consisting of his team, a few marines and few wraith, including Todd.

Lorne had broken off to deliver his report to Weir and Caldwell. Once he'd taken a seat in the conference room, the Major went into detail about the events leading up to John's rescue and the details of the rescue itself, then onto the things that happened on the hive ship afterward.

“You can say for certain that's the real Lieutenant Colonel John Sheppard and that he hasn't been brainwashed or anything?” Caldwell asked. “You did say he developed telepathic abilities. For all we know, Michael could be controlling him like a damn marionette.”

“I don't think Michael can,” Lorne said speculatively. “If he could control John, he would've done it during one of his escape attempts. And they were real escape attempts before you throw that out there. He almost succeeded, or rather he came uncomfortably close. He had the Colonel in the Jumper, the two of them fighting. He could have just taken him and flown out of there if he could control him, but he didn't.”

“Okay,” Caldwell sighed. “What happened during their fight?”

“Michael got the upper hand, unfortunately. I guess we're sort of lucky that he decided to... celebrate his newfound freedom before trying to leave the hive.” Lorne cleared his throat, not wanting to put what happened to John into words.

“Care to elaborate?” Caldwell asked

Lorne sighed heavily. “Michael raped the Colonel after he'd wrestled him down in the Jumper,” Lorne said softly.

Elizabeth sat back in her chair, slacked-jawed, while Caldwell just went quiet.

“Oh, my god,” Elizabeth breathed. After a few moments of silence, she continued with a question. “Why?”

“That's where things get complicated,” Lorne responded slowly. “It has to do with what Michael did to him in that lab. It's completely insane, and hard to believe, but long story short, Colonel Sheppard is a hermaphrodite now.”

“What?!” Elizabeth exclaimed, her face a mask of shock.

“What does that mean, exactly?” Caldwell asked.

“A hermaphrodite is someone with both male and female genitalia,” Elizabeth answered. “Typically, it's a male who’s been turned into a female. There are hundreds of creatures in the animal kingdom that can do it naturally, usually based on necessity. Why would Michael do this to John?”

“We don't know,” Lorne said. “He's been pretty tight-lipped about everything he did and why. He does, however, keep asking for his 'mate'.”

“He thinks John's his mate?” Elizabeth asked. “Wraith don't have mates, nor do humans. Why would a human-wraith hybrid?”

Lorne shrugged. “I have no idea. You'll have to talk to Todd and Dr. Beckett about that. They seem to have some theories.”

“Okay,” Elizabeth said. “Is there anything else we need to know?”

Lorne hesitated again. “Todd and his crew want John to stay with them and be a queen for their hive. Also, apparently, Michael has raped the Colonel more than once, because he's pregnant.”

Silence fell over them once again.

“Colonel Sheppard is very conflicted about the whole thing, and Michael is practically losing his mind trying to escape and take the Colonel with him because Todd went ahead and told him that the Colonel is pregnant. I don't know why,” Lorne continued. “Dr. Beckett has offered to terminate it for the Colonel, but Todd is being very resistant to giving Colonel Sheppard that option. It's all very complicated and I don't know what to make of most of the situation. You need to talk to Colonel Sheppard about this, not me.”

Elizabeth was silent, apparently taking in all the information. Caldwell was tapping his fingers on the table in irritation.

“What am I supposed to do with this situation?” Caldwell asked them both, turning his head between Lorne and Weir. “As far as I'm concerned, John Sheppard is compromised and should be detained.”

“I think we should just keep Michael detained, and see how things play out for John,” Elizabeth decided. “He'll have to be removed from active duty anyway, but I really don't think he should be imprisoned by his friends and colleagues, especially after he's just been liberated from Michael.” She looked directly at Colonel Caldwell, who sighed and threw his hands up. 

“Fine,” Caldwell said. “But if this blows up in our faces, I am not taking the blame.”

“That's fine,” Elizabeth said, standing up and pushing her chair in. “This meeting is over. I need to go talk to John.”

To be continued.

**Author's Note:**

> I wonder what Joe Flanigan would think if he read some of the shit people have come up with for him in these SGA fanfics...


End file.
